晶体生长过程视频课件

Growing X-ray Quality CrystalsPaul D.BoyleDepartment of ChemistryNorth Carolina State University15 November 2006.Topics to be CoveredThe Objective:Getting“Good”CrystalsWhy do you need good crystals anyway?The Right Attitude toward crystal growingFactors affecting crystallizationCrystal growing techniquesQuestions and Answers/Discussion.Objective:Getting Good CrystalsA“good”crystal is:0.1-0.4 mm in at least 2 of its dimensionsexhibits a high degree of internal order as evidenced by the presence of an X-ray diffraction patternVery often,but not always shows regular faces and edges.Why do you need good crystals anyway?Quality of sample characterized by maximum diffraction angle(q)-also expressed in“resolution”()The larger the max.diffraction angle,the greater the resolution and the greater number of data(which is necessary to adequately model the structure)Discerning individual atomic position requires data resolution which is greater than the bond lengths between the atoms(.e.g C-C=1.54).The Effect of Limiting the Resolution of the Data.Effect of Limiting Resolution of the DataElectron Density Map using all available data(qmax=32.35)Resolution=0.66 All atomic positions are easily resolved.Limiting the Resolution of the DataLimited qmax=25.0Resolution=0.84 Peaks are beginning to flatten outAtomic positions are still easily resolvableIUCr recommended minimum resolution.Limiting the Resolution of the DataLimited qmax=19.47Resolution=1.5 Peaks start to“melt”into each otherIndividual atomic positions are still resolvable.Limiting the Resolution of the DataLimited qmax=14.48Resolution=2.0 Metal position resolvableOnly gross shape of organic ligand evidentPeak positions for ligand have shifted away from true atomic positions.Limiting the Resolution of the DataLimited qmax=11.54Resolution=2.5 Metal position still discernibleIndividual atomic positions for ligand have been lostLost of chemically useful information.Limiting the Resolution of the DataLimited qmax=9.59Resolution=3.0 Only metal position is discernibleLigand is completely“washed out”.Limiting the Resolution of the DataLimited qmax=8.21Resolution=3.5 Metal electron density is“bleeding”into the traces of the ligands electron density.Limiting the Resolution of the DataLimited qmax=7.18Resolution=4.0 Metal position is only barely above backgroundNo trace of ligand.Limiting the Resolution of the DataLimited qmax=6.37Resolution=4.5 Metal position cannot be differentiated from noise.Limiting the Resolution of the DataLimited qmax=5.74Resolution=5.0 Noise.The Right Attitude toward Crystal Growing for X-ray AnalysisGrowing X-ray quality crystals requires care and attention to detailDont treat crystal growing in an offhand or casual way(forget what you learned in undergraduate organic chemistry labs)Treat it like its own miniature research projectDont try to skimp on the amount of material when growing crystals.General Approach to Growing X-ray Quality CrystalsPurify your compound(using conventional crystallization and/or other purification steps)Consider the empirically established physical properties of your compound sensitivities,thermal stability,etc.Develop a solubility profile of your compoundUse CLEAN glassware as crystal growing vesselsSet up crystal growing attempts in parallel utilizing different conditions.Purify Your CompoundImpure samples do not recrystallize as well as pure samplesRecrystallization minimizes the presence of foreign insoluble material which increases the number of nucleating sitesSuccessive crystallizations purify the compoundAlways use recrystallized material when setting up a crystal growing attempt.Solubility Profile.Use CLEAN GlasswareClean glassware should sheet water uniformlyUse KOH/EtOH bath or aqua regia to initially clean glassware and rinseFollow by soap&water washingFollow by acetone or MeOH rinseOven drying.Parallel Crystal Growing AttemptsCombine knowledge of solubility profile with crystal growing techniquesSet-up simultaneous crystal growing experiments.Factors Affecting CrystallizationSolvent moderate solubility is best.Supersaturation leads to sudden precipitation and smaller crystal sizeNucleation fewer nucleation sites are better.Too many nucleation sites(i.e.dust,hairs,etc.)lower the average crystal sizeMechanics mechanical disturbances are bad.Time faster crystallization is not as good as slow crystallization.Faster crystallization higher chance of lower quality crystals.Solvent ConsiderationsModerate solubility is best(avoid supersaturation)Like dissolves likeHydrogen bonding can help or hinder crystallization.Experiment!Presence of benzene can help crystal growthAvoid highly volatile solventsAvoid long chain alkyl solvents can be significantly disordered in crystals.Choose solvents with“rigid geometries”(e.g.toluene).Nucleation&GrowthCrystals initially form via“nucleating events”After a crystallite has nucleated it must growNucleation sites are necessary,but.Excess nucleation sites cause smaller average crystal sizeAmbient dust,filter paper fibers,hair,broken off pipette tips all provide opportunities for nucleation take steps to remove them.Mechanics(Crystal Growth)Crystals grow by the ordered deposition of the solute molecules onto the surface of a pre-existing crystalCrystal growth is facilitated by the environment changing slowly over time.Keep crystal growth vessel away from sources of mechanical agitation(e.g.vibrations)Set-up away from vacuum pumps,rotovaps,hoods,doors,drawers,and so onLeave samples alone for 1 week,dont“check in”with it.Your crystals are not lonely.TimeQuality crystals grow best over time in near equilibrium conditionsThe longer the time,the better the crystalsPatience,patience,patience.Crystal Growing TechniquesSlow Evaporation:simplest to set up.Has drawbacks:solute can“oil out”,crystals stick to sides of vessel making them difficult to extract from vessel without breaking them.Slow Cooling:Soluble when hot,insoluble when cool.Use Dewar to slow the cooling process.Variations:use binary or tertiary solvent mixtures.Use solvent with similar b.ps and other properties.Vapor Diffusiondissolve solute in solvent(purple)precipitating solvent(blue)blue should be more volatile than purpleDont let sides of small vessel touch vertical surface of outer vessel(prevent capillary action).Solvent DiffusionGood for milligram amountsUse NMR tube for best resultsFill soluble more dense solvent on bottom with your solute.Fill the rest of tube with less dense precipitant solventE.g.CH2Cl2/Et2O.Reactant DiffusionSet-up similar to solvent diffusion except that reactants are in different layersGood for milligram amountsGood for completely insoluble products which never go back into solution after being formedConsider using a 3rd“middle layer”solvent to mediate the reactant concentrations.Sublimation(1)Gas to solid phase crystal growthCompound needs to be thermally stableCan be easy to set up vacuum sealed tube of material placed in oven for several days/weeksOr more complicated material packed in tube followed by glass wool.Place under active or static vacuum and set-up thermal gradient by heating the loaded end of the tube.Place Cu pipe around tube to create thermal gradient.Sublimation(2)Specialty sublimation glassware availablePerform slowlyUse small amounts of material.Convection(Principles)Create a thermal gradient in the crystal growing vesselSolvent becomes saturated in“warm”region and deposits material in“cool”region where nucleation and crystal growth can occur.Cyclic current allows continual replenishing of soluteVelocity of convection current is proportional to the magnitude of thermal gradient.Take care that gradient isnt too large too high velocity inhibits crystal growth.Convection(Easy Way)Local cooling simple to set upTake flat bottomed crystal growing dish and set up like slow evaporationPlace vessel so that one side is against a heat sink,e.g.an outside window(in Winter at least)Placing crystal growing dish on a cool surface will not cause convection.Convection(Special Apparatus)Fill Thiele tube with solvent.Wrap nichrome wire around the bottom side arm and attach to VariacPlace solute is small container just below top side entranceApply heat.Co-CrystallantsSometimes two(or more)different compounds“co-crystallize”.Most commonly,this is a solvent moleculeTriphenylphosphine oxide has been used as a co-crystallant for both inorganic and organic compounds.Chemical ModificationFor ionic compounds,change the counterion to change the solubility and other characteristics of your compoundIons of similar sizes tend to pack together betterUse counterions with rigid geometries e.g.triflate,BPh4-,Me4N+,(Ph3P)2N+Tend to disorder:Et4N+,Bu4N+,BF4-,PF6-Make sure counterion does not react with your compound!.Chemical Modification(Ionization of Neutral Compounds)If your compound is neutral and has proton acceptor or donor groups,consider ionizing the compoundThe ionic form make take advantage of hydrogen bonding to give better crystalsCounterions can be changed to optimize crystal growthThis will change your compound,but if you are only interested in confirming a structure,and not in detailed electronic properties,this shouldnt be a problem.Online ResoucesUse google(around 39,000 hits for X-ray“crystal growing”),the knowledge is out there!http:/www.xray.ncsu.edu/GrowXtal.htmlhttp:/xrpc4.harvard.edu/xtalgrow.pdfhttp:/xray.chem.ufl.edu/growing%20tips.htmhttp:/www.cryst.chem.uu.nl/growing.htmlhttp:/xrayweb.chem.ou.edu/notes/xtalgrow.html.ConclusionThe quality and meaningfulness of your results is directly dependent on the quality of your sample crystalYou can get information from a bad crystal structure,but it will be difficult to publishTake crystal growing as a serious part of your research project spend the time and effort to be successful.There are many solvents and crystal growing techniques available use them.