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12/22/2020Getting Crystals YourCrystallographer Will TreasureRichard J. StaplesCrystallographerMichigan State UniversityWhat is a crystal structure? The determination of theconnectivity of the atomsin a compound and theway the molecule (ormolecules) pack to form asolid crystalline material.1

12/22/2020What is gained from a crystalstructure? Positive identification of a singlecrystal. Exact connectivity. Bond distances and angles. Complete identification of thecompound. Inter molecular interactions. Intra molecular interactions.What do I need to bring to theLaboratory? Single CrystalsBring what you can growChemical FormulaCompound NameIf not single--- Discussrecrystallization2

12/22/2020Solids and Crystals Solids Crystalline Material which internally Possess long-range three dimensional order.Examples: table Salt, Sugar, gems, Quartz, Metals Non-crystalline Amorphous, short-range ordered, or random ordered materials, ‘super cooled liquids’Examples: Glass, 1 or 2 D ordered solids, fibers, liquid crystals.Crystals - Single Crystals Single Crystal lattice is well defined with small repeating units in three dimensions.Properties:Extinguish on rotation of cross-plane polarized lightClear, generally sparklyNice regular shape, faces and edges.3

12/22/2020Crystals, Non- Single Non-Single A lack of well defined repeating units, may be systematic. Properties of well defined Non-single crystals, Twins Clear view of two extensions under plane polarized light.Symmetry related and definable operations resulting in a well defined lattice.Crystal Size Size should be 0.05 x 0.05x 0.05 mm perfect. Gives 0.87 mm diagonal. Smaller crystals are verypossible! Larger crystals can becut!4

12/22/2020Techniques for Growing Crystals Key factors in obtaining good crystals. Read: “Crystal Growing”, Peter G. Jones,Chemistry in Britain, 17(1981) 222-225. See www site by Paul D. Boyle(http://www.xray.ncsu.edu/GrowXtal.html). “Some thoughts about the single crystal growth ofsmall molecules” B. Spingler, S. Schnidrig, T.Todorova and F. Wild Cryst. Eng. Comm., 2012, 14,751-757. Various techniques.Where Do I Start? SimpleRecrystallization. During Purification didyou create crystallinematerial? Are these crystals Bigenough?These crystals were 0.05 x 0.025 x0.002 mm5

12/22/2020How much Material Do YouNeed? Depends on the vessel youare going to use to grow thecrystals. Depend on Solubility ofsample in the solvent. NMR sample Generally a goodconcentration level.How much Material is in a SingleCrystal? If the crystal for x-ray diffraction is to be 0.3 x 0.3 x0.3 mm, volume 0.027 mm3 Typical unit cell is 12 x 12 x12 Å; volume 1728 Å3 Å3 10-10 meters 10-8 cm 100 pm ( picometers) Therefore in a typical crystals 1.6 x 1016 unit cells 1.3 x 1017 molecules for 8 molecules per cell. MW 206.2 then only 2.49 x 10-7 moles in thecell. 5.1 x 10-5 g, 0.051 mg Unfortunately more than one crystal grows in thevessel so more material is needed.6

12/22/2020What is the Goal To Create a single crystal which diffracts on theinstrument such that an analysis can beaccomplished. Generally this means to get the material to go fromsolution to a solid very slowly. Create an environment that slowly changes over timeto cause crystallization.What do I grow the Crystals In? Clean glassware, most of thetime. Consider location Consider volume needed togrow the crystal. Usually clean new vials that fitinside one another work well.7

12/22/2020Solvent Choice Polar--- polar solvent layered with a non-polarsolvent Non-polar --Non-polar solvent, evaporation or layerwith polar solvent, harder.Hydrogen Bonding Hydrogen Bonding is very important in thecrystallization process. Consider whether hydrogen bonding solvent mighthelp or hinder crystallization. Amides generally do better with hydrogen bondingsolvents.8

12/22/2020Solvents to Use and NOT to Use Use Benzene! Seems to be a magic solvent. It hasbeen seen that toluene can do the same sort ofthing. Aromatic rings seems to help fill holes in lattice aswell. Ethyl Acetate works for a lot of compounds. Avoid volatile solvents, CH2Cl2, Diethyl Ether. Avoid long alkyl chains, cause disorder.Solvent Layering Layering must be very careful. Place a solvent between the two layers. Do Not disturb the vessel. Set it so you can view it without moving it.9

12/22/2020Example of Layering Grown by layering asolution of methylenechloride with pentane.Staples, Swiatek Z. Krist.Vapor Diffusion Good for milligram amounts.Volatile solvents.Slowly create a less desirable solvent.Need to be aware of vapor pressures of solvents.10

12/22/2020Example of a CrystallizedCompound from Vapor Diffusion Used a diffusionchamber withcompound in thedichloromethane andthen hexane in theoutside chamber.Evans’s group, CH2Cl2/hexaneSlow Evaporation Allow the material tocrystallize out as thesolvent evaporates. Keep the solution cleanand covered to avoiddust particles.Holm’s Group, Evaporation of acetonitrile over several days.11

12/22/2020Use The NMR Tube Often Crystals havebeen received byallowing the solvent toevaporate slowly fromthe NMR tube. Remember to keepthe tube covered toavoid dust and dirt.Holm’s Group, Left in NMR tube overnight, Benzene-d6Slow Cooling Standardrecrystallizationtechnique. Must perform thisslowly to work well. Slow reduction of thetemperature is best.Grocholl, Huch, Stahl, Staples, Steinhart, Johnson Ingor. Chem. 1997, 36, 4451.12

12/22/2020Sublimation Works extremely wellwhen can be done. Must be performedslowly to achieve goodsize crystals.Vij, Elias, Kirchmeier, Shreeve, Inorg. Chem. 1997, 36, 2730-2745.Chiral Compounds These tend to be moredifficult. Try to makederivatives which willimprove packing. i.e.phenyl rings. Have atoms heavierthan carbon.Evans’s group, CH2Cl2/hexane13

12/22/2020S-alpha-methylbenzylamine Use with carboxcicacids, could begenerated from alcoholor aldehydes. Cheap and usually easilycrystallized.Aldehyde converted to acid then to the amide.Corey, Lee Tetrahedron Lett. 1997, 38, 5755.Improve heavy atom andCrystallization Have heavy atompresent. Alcohols and Aminesmake derivative withp-Bromobenzoate Include aromaticcomponents inderivative.Crystal was 0.1 x 0.05 x 0.05 mm,grown benzene layered with hexane.14

12/22/2020Heavy Atom Present In some cases you can make a salt and have theheavy atom be the anion or cation.Corey, Xu, Noe J. Am. Chem. Soc. 1997, 119, 12414-12415.Counterions or Ionization Change a counterion in thecomplex. Ions of the same size tend topack well. If neutral compound does notcrystallize or is liquid, create anion. Deprotonation orprotonation. Good to confirmthe identity of the material.Corey, Xu, Feng, Noe JACS 1997, 119, 121415

12/22/2020Reactant Diffusion Perform the reaction on a small scalecompared to surface area. Layer one reactant on top of the otherreactant and allow diffusion to controlreaction rate and crystal formation. Good when product formed is highlyinsoluble.Odd Methods Melting the compound and letting itrecrystallize! Seeding a solution with similar crystallizedmaterial.16

12/22/2020Key Factors to Good Crystals. SolventNucleationMechanicsTime Patience, Patience Art Form17

12/22/2020What is a Good Crystal? Well defined crystallineshape often results ingood crystals. Sparkle One that works!! Gives good spots and spotshapes.Crystal Evaluation Evaluation starts at themicroscope. Do they lookcrystalline and single under crosspolarized light? Are all the crystals uniform inshape? Do they start become less definedover time, loss of solvent. Mount and evaluate the crystal onthe diffractometer. Requiresabout 20 - 30 minutes. Less if itdoes not diffract at all.18

12/22/2020Manipulation Tools for Crystals Varies withcrystallographerand type ofcrystals. Have a variety oftools so you canchose theappropriate one forthe occasion.You can purchase expensive toolsto do the job.Manipulation Tools Common Good standard probetools from biologywork well. Some like to usedental tools, can getthem free after thedentist is done withthem. Some use glass fibersor needles.19

12/22/2020Manipulating and Cutting Crystals Cut the crystals to size. Use a new blade, nice sharp edge. When cutting do they crumble, these are not likely single. Use of a scalpel or X-acto knife works well. Razor blades are some people preference. A Sapphire knife is expensive, but worksreally well for small or fragile crystals.Where to manipulate the crystal Often done in an oil Considerations for choiceor solvent grown in. Are you running low temperature Does the compound dissolve Paratone Oil Mineral Oil Greases, normal andfluorinated. UV curable Epoxy Radiation using Do you need to cut the crystals Does the crystal degrade, or is air sensitive20

12/22/2020What happens tolarger crystals? Cut the crystals to size. When cutting do theycrumble, these are not likelysingle. Do they start become lessdefined over time, loss ofsolvent.How do you mount the crystals? Use a small amount of paratone oil,Mineral oil or T-grease. LowTemperature Very small crystals, try using a loopor a micro mount. Use various adhesives Glue– Room Temperature ( see later)21

12/22/2020Thoughts on Crystal Mounting.– Try and not to create flags withfibers.– Micro Mounts, place on innercurved side.– Use as little grease, oil, or glue aspossible.– Try not to orient in direction ofmount.Mounts and GoniometersVarious mount types depend on the instrument and goniometer you are using.22

12/22/2020Gluing for Room Temperature RTV118 (Momentive) This is great to do roomtemperature and low temperature datacollections. (Si Based) Seems not to crack when going to lowtemperature. Expensive Super Glue Caution acetone solublecompounds. Need to work quickly Epoxy 3- 5 minute epoxy, good for airsensitive compounds, generally higherbackground Can do this for Low Temperature Collection, but cleavage can occur, and crystalfalls off mount.Getting Crystal on Fiber or LoopAll Crystallographers have their own method to accomplish this task.Some will work for you and some may not work as well. These twomethods work for most students at Michigan State University, runninglow temperature data collections.Slide methodPlace the crystals in a small amount of Paratone oil. Slide thecrystal out of the oil until the crystal prefers to stay on the fiber. This is used wellfor large crystals mounted on fibers.Pick upTry and put enough oil on the fiber that the crystal comes withthe oil. This method means you should try to remove excess oil before placing ondiffractometer. Good for loops. Slide method also works for loops with smallcrystals.23

12/22/2020Mounting to loop in solventMounting Crystals In CapillariesA) Assemble capillary, syringe and rubber tubing.B) Under a low power-dissecting microscope, draw thecrystal into the capillary.C) Remove excess liquid with a paper wick.D) Apply crystallization media to either side of the crystal(or both) in order to prevent desiccation of the sample.The capillary is broken at the location of the wax bead andthe open ends are sealed with wax or vacuum grease.24

12/22/2020Mounting on A FiberMounting to loop in solvent25

12/22/2020Crystal Needs to be in the center ofthe BeamSimplified Goniometer26

12/22/2020CenteringSometimes the cross hairs do not represent the center of the x-ray beam and so rotationof the crystal by 180 degrees is done to facilitate alignmentRotation by 180 degreesAll modern instrument have a waythat you rotate the sample withrespect to the video camera ormicroscope, such that you canrotate a perpendicular view by 90and 180 degrees. This allows youto center the crystal in the beameven if the center of the videocamera or microscope is notcorrect.27

12/22/2020Rigaku SOFTWARECentering28