Reprinted from Chemistry in Britain, Volume 17, Number 5, May 1981 Crystal growing Peter G Jones In recent years structure determination by x-ray crystallography has crystals for method 7. The seed crystals become a commonly used technique in chemistry, largely due to the stovld be drawn off ino pipette together development of automatic diffractometers, powerful computers and With some mother quor allowed clegant programs. More and more chemists are thus encountering the [0 ._ssed__cnstls los thoy technique and need to familiarise themsclves with some of its funda- _“fectivaness_and wun nwo, he worm mentals. Since most institutions have specialist crystallographers to tyre ‘crue vary lagu enysale (oo deal with the technical problems of data collection, structure solution eral mm) or neutron traction, 9 land refinement, the essential role of the chemist is often restricted to General rule. the fewer the seeds. the the provision of suitable crystals. eeatie suuien eraai Crystal quality The quality of crystals cannot be instantly recognised in situ: examination with 2 microscope is necessary. Remove some ff the crystals from their mother liquor {and place them on a slide. Do not remove all of them, even if the compound is known to be air stable, because crystals cften decompose by loss of solvent of crystallisation once out of contact with the mother liquor ‘A. 9006 single crystal will normally have well-formed, clea faces; a crazed or fibrous. appearance is an indication of Fig 1) The Hguid difusion method, @) OO! qUaliy. If crystals have grown in Aithough many compounds emerge rom preparative procedures in ‘crystalline form, these crystals are rarely suitable for structure determination. The following special procedures are often used 10 prepare good single crystals, 1. Slow cooling of saturated solu. tions. The flask and solvent to be used should be dust-free. The flask of warm solution is allowed 10 coo! in a Dewar of warm water over a period of several days This classical method often gives results ‘when method 2s inapplicable (eg when the compound is soluble in most liquids) 2. Liquid diffusion. This is normally Shation ef compound to be ceystalived, CUMS, single crystals may often be the most successful method of abtaining Gi Slowly layer om the precipitant, Separated with a needle, or cutoff with a single crystals (see Fig. 1). A small Gr) Stopper and leave overnight: Do not scalpel or azor blade. To prevent crystals ‘amount of solution is placed in the tube disturb. (») Crystalsform atthe interface. from flying off and becoming lost, they ‘anda suitable precipitant is layered care- the same asthe previous method, but the ca be anchored to the slide with a trace fully down the side of the tube on to the precipitant is allowed to diffuse into the of silicone grease solution. This second liquid should be Solution from the vapour phase (see Fig. Hf a microscope with polarising less dense than, and miscible with, the 2), Advantages of this method are that attachment is available, the identification solvent. The tube is then corked and left several tubes may be set up in the same Of good crystals is made much easier tostand undisturbed for 24 hours.Asthe container (@ sealed desiceator is often When @ good single crystal is viewed precipitant diffuses into the solution, Ysed) and thet very small quantities may between crossed pola (te black back Crystals form atthe interface. A sultable be used (on @ soot plat) Crystal form, 9F0UNd) wil probabiyshow upright: Solum ratio solvent/prciptant is 1:4 tons somewhat slower (several doy) 2. the vapour aithaton method. ( 91 1:5; the solution should be sut- "4. Convection methods. A simple ap: ‘Sdlution of compound to be cryatallicd, feienty concentated to form an im- poratis inverted by Hope’ t besed on (a) Introduce: precipitant and stopper mmacate turbidity atthe interface. "no Goruineaus convection (eg. 3), Smiye ti) Grbstate form afer somne Crystals have formed in’ 24 hours. ty "8. Difusion ‘ef resting solutions. day agen with 2 stronger solution. Compounds arisna es precipitates, by Common.” used “solvent/oeciptant —fegcton of two solutions may ofen be pairs ae water acetone: chloroform of Qhtained In erysaline form by lyerng tethyiene chleide/petoleum ether © gnereectingsoltion on tne other. bath cyloherane: and. | have had reactants ate in the somo solent. the Considerable success with formic _jayering may be facilitated by adding ‘acid/diisopropy! ether. This method is small amounts of other liquids to adjust ‘also suitable when only small quantities the densities. A ‘buffer layer’ of pure ‘of material are available (2bout 0.1 mi solvent ora fine porosity frit may be used solution is quite adequate) to prevent excess immediate precipita ‘3. Vapour diffusion. The principle is tion, This method is slower than 2 because teaction must be complete oan before the mixture is disturbed Ehomisebos”Inettun "Gar "Oreeeeiat 6. Use of seed crystals. I other meth ‘Tammannsty 4, 3400 Gottingen, Federa’ | ods provide crystals which, although of Repuoic of Germany. Feasonable quality: are too small, then these may profitably be used as seed 222A ypical organic crystal structure determination yields this picture of the natural Product loganin. Carbon and oxygen atom are represented as thermal ellipsoidsof SO per eat probability (ie there is #50 per cent chance of finding an atom ions). Hydrogen atoms are plotted as spheres of constant radiu ‘daring its thermal vibr ‘on rotation of the slide, all parts of the ceystal should extinguish the light sharply and simultaneously. (Cubic and some other high symmetry crystals are rare exceptions to this behaviour) If one part of the crystal is bright and another partis dark it is probably not a single crystal, The crystal must of course be transparent for this procedure. Crystal size and shape are important. Equidimensional crystals are best, though plates or needles may often be used. The optimum size and shape are determined by the type of atoms present. Itonly light atoms are present, eg typical organic structures containing carbon, nitrogen, oxygen and perhaps a few phosphorus, suiphur or chlorine atoms, the crystal may be of medium to large size, in crystallographic terms, about 0.3 to 0.7mm in the longest ditection, (Few diffractometers can provide a uniform x-ray beam larger than 0.8mm diameter, and it is essential that the whole crystal always remains in the beam) If heavier atoms are present, the crystal will absorb x-rays to an’ ap: preciable extent; large crystals cannot then be used because few x-rays will get through! By way of compensation, how. ‘ver, such materials usually diffract x rays more strongly, so smaller crystals are quite usable. A suitable size would be 0.1 to. 0.3 mm maximum, depending on the ‘heaviness’ of the atoms present—a crys- tal as small as 003mm may be adequate it it is very strongly diffracting The effects of absorption are enhanced 224 id thin its elips by extremes of shape such as plates or needles, and these shapes are therefore best avoided (reflected beams will be attenuated much more when passing ‘along the long axis of a needle than when perpendicular to i). Modern programs are, however, capable of applying atfec: tive absorption correctionsin most cases Finally, when you have obtained reasonable-looking crystals, take them (at least some still in the mother liquor) 10 your crystallographer. He can then decide whether to mount them with mother liquor in a capillary: this is not usually done unless necessary, as the capillary scatters x-rays, leading to. high background level and less precise measurements. Since the waiting list to Use the diffractometer may be several months your compound, even if “air stable’, may decompose over this period | have suffered several disappointments {due to sublimed or hydrolysed erystas! If your crystals are ata likely to misbehave, warn the crystallographer, Why do you want the structure? Before requesting an x-ray structure itis as well to ask yourself exactly what you want to know. There are three main reasons for wanting a structure. 1. To identity an unknown compound. ‘Although crystallography is becoming 3 routine analytical technique, it is still lume- and resource-consuming. It is therefore best to exhaust other, more conventional, approaches (ir, nmr, ele mental analysis) first, Even if the exact ature of the compound is unknown, any information (eg what elements are pre- sent, whether the compound is optically active) will help the crystallagrapher 2. To obtain accurate interatomic dist: ances and angles. For normal organic structures with no elements heavier than Chlorine, bond lengths and angles will probably have an accuracy af 0.008 A, 0.5" or slightly better. However, since x rays are diffracted by electrons, any atoms appreciably lighter than the rest ill be less accurately located —if at alll Thus, hydrogen atom positions will be relatively inaccurate in organic structures (C—H bond lengths to accuracy 0.02 A fF less). In the presence of heavy ele ments (eg the heavier transition ele ments) firstrow elements will be similarly affected and locating hydrogen atoms is usually impossible. 3. To determine the absolute configur: ‘ation of a chiral compound. This s less common, but still important requirement. ‘The determination of absolute configur- ation depends on the measurement of small intensity differences between re- lated pairs ofreflections;thesedifferences ate greater (and the determination thus facilitated) (/) when heavy eloments are present and (ji) when longer wavelength fadiation is used. With copper radiation (1.54 A) the absolute configuration may, ‘with luck, be determined when only fist row elements are present. Modern prac- tice is however to use molybdenum radi- ation (0.71 A), which is absorbed less in this ease bromine or heavier elements will probably be needed Choice of compound To some extent the chemist may have several possiblities open to him in ‘choosing @ compound for x-ray analysis, eg different side chain substituents, Fig. 3. Apparatus for crystal growth by convection. The substance of which erys- tals are required is placed at the bottom Teft. A and B are heating coils and Cis 4 cooling coil. Crystals form near Cand are carried to the bend (bottom right) bycounter-ions or solvates. A sensible choice may make both his and the Ceystallographer's work much easier. The following quidelines should therefore be observed if at all possible. 1. Try to reduce the possibilities of dis. order. X-ray analysis assumes that the contents of each unit cell are identical. if (groups are tree to rotate, or can occupy different positions in different cells, this assumption is only tue in an average sense and svucture refinement can become difficult. This phenomenon is known as. disorder. Relatively small, highly symmetieal ions (eg BF, ClO, PF, SO,F") are unlikely to partake in stwang secondary interactions such as hydrogen bonds and are thus often dis: ordered: bulky ions (eg Ph,As', (Ph,P),N~, BP, picrate) are less likely 10 rotate freely and their use as counter- ions is strongly recommended. Similarly, torsionally symmetric groups such as CH, CF, PO, (especially when bonded to 5p? atoms and therefore experiencing no torsional energy barrier) and long (CH,),CH, side chains (asin sterols land many other natural products) are ‘often disordered. The most recommen- ded substituent 's phenyl: this is rarely disordered and has the additional ad vantage that phenyl derivatives often exystallise more easly 2. Avoid low melting point solids or liquids. Low temperature x-ray work, although possible, is often beset with ‘The problems engendered by the use of highly symmetrical, small ions. This isan Sb,” ion, which shows a virtually spherical distribution of its F atoms, It Inas been refined as if it were occupying two different sites, but the large sine of the F ellipsoids shows clearly that the dis- order must be more severe. (am grateful to Dr Gabriela Weber for this example). practical difficulties and always requires frequent attention Low melting point solids, if not cooled, often exhibit some form of disorder due to their high thermal 3. The choice of solvent is often dictated by what will give the best crystals, Solvent of crystallisation may, however often be disordered, especialy for sol vents such as benzene, CHCI,, and CH,Cl, which form no strong secondary interactions to other molecules. tis usu- ally best to get crystals fist and worry about this later. 4. Fifteen years ago the solution of an organic. crystal structure normally de. pended on the incorporation of a heavy ftom (often iodine or bromine) into the structure, Vastly improved structure solv- ing methods now tender this unnec- essary, and it can in fact often be a disadvantage; the precision of light atom location is reduced, and organic bromides and iodides often decompose ‘when irradiated 5. Make sure the compound isthe right ‘one! Simple checks may be possible, egt the compound is meant to contain phos horus and fluorine, check its) nme spectra. Your friendly local erystallograp- her will not be amused if time is wasted fon the wrong structure, and this happens more frequently than one might imagine, 6. Check that the structure has not been done before! The Cambridge Crystallographic Data Centie reviews yearly all structures containing at least fone C—H bond (Molecular structures ‘and dimensions); inorganic structures are presented in the si0ics series of publi cations from MeMaster University, Canada. Both should be in most un iversity chemical libraries Reference 1. Hope, J Appl Cryst. 1971, 4 333.