5 From crystal to cif Get crystal Short experiment to index Long experiment to collect complete dataIntegrationAbsorption correctionIdentify space groupSolve You start hereRefineCif
6 What is crystallography all about A crystal is a 3D periodic array of moleculesX-rays interact with (diffract from) electronsDiffraction results in a regular pattern of spots (due to constructive and destructive interference)Intensities observed are related to atom types and positionsWe build a model and compare the calculated diffraction pattern with the observed
8 What you will get from us 2 or 3 filesins fileThe shelx instruction file contains unit cell, radiation wavelength, temperature, crystal system and space group information, unit cell contents from user inputhkl fileThe reflection data, contains indexed intensities with associated estimated standard deviationscif fileContains some experimental details (not essential)
9 Files – ins file TITL pg24 in P-1 CELLZERRLATT 1SFAC C H N S HGUNITPATTHKLF 4END
11 Structure Solution We need to get an initial model from which to work This is called structure solutionWe can only measure intensity but we really want to know the phase of each reflection.Several methods of extracting initial estimated phases from our data are available.
12 Structure solution Direct methods Requirements How it works It is desirable but not required to have a centrosymmetric structure.How it worksUses statistical relationships between the intensity of different reflections to establish phases.Look out for…This is a very powerful method which often works very well but as it is based on statistical analysis, it will sometimes fail.Computationally demanding. Scales inversely with symmetry, i.e. low symmetry large unit cells take more time.
13 Structure solution Direct Methods Programs xs from the shelx suite (works for me 99% of the time)Instruction is TREFYou may specify a number after TREF to increase the number of trials for difficult structures.Sir softwareSeveral versionsSir92, Sir97, Sir2002, Sir2004May get different results with different versionsVariety of options for structures of different size/difficulty ORCan be set up through, e.g. WinGX for simplicity but less control.
14 Structure solution Patterson Methods Requirements How it works A heavy element, e.g. Fe, Cl, S, etcHow it worksGenerates a map of ‘peaks’ representing difference vectors, i.e. interatomic vectorsPeak intensity is related to the product of the atomic numbers of the two atoms involved thus the heaviest elements are identifiable.Look out for…Depending on the program you may only get the heavy atom positions. Completing the structure may take more time and effort than e.g. Direct methods
15 Structure Solution Patterson Methods Programs xs from the shelx suite Instruction is PATTYou will only get heavy atom positions backDirdifWill attempt to complete the model and guess atomic assignments.Can be extremely useful for complicated metal clusters, etc.
16 Structure Solution Partial Structure Expansion Requirements Knowledge of expected substructures and their geometries, e.g. a benzene ringHow it worksUses a Patterson map and rotates the substructure around three axes until a best fit is found to the data. There will then be attempts to complete the model using the phase information from your partial structure as a basis for phase refinement.Look out forNot many pitfalls assuming you are confident of the unit cell contents.More time consuming to set up than other methods and unsuitable for unknown samples.
17 Structure Solution Partial structure expansion programs PATSEE from the wingx suiteYou must provide a list of coordinates for your substructure.DirdifProvides a small database of common geometries e.g. benzene rings, indoles or can use your own.Not necessarily user friendly in my opinion
18 Structure solution Charge flipping Requirements How it works Complete data (at the moment)How it worksUse random phases, ‘flip’ the sign of electron density charge below a threshold and get new phases. Use new phases with original magnitudes. Repeat.No symmetry is used for solution. It is determined afterwards.Look out for…Unreliable results with incomplete data
19 Structure solution Charge-flipping software Superflip Flipper From originators of the methodAvailable as standalone (not recommended), via WinGX, via crystalsFlipperAvailable in Platon
20 Structure solution Has it solved? Use your chemical knowledge… How atoms interactE.g. expected bond distances and angles for particular arrangementsReactions or decompositions which may occurNon-bonded interaction lengths and typesE.g. +ve to +ve is not going to be commonChargeShould always be neutral for a unit cellAssignment of charge on metals, ligandsLikely patterns of motionE.g. neighbouring atoms are likely to have similar thermal motionSpinning or wagging of certain groups may be expectedGroups which are likely to be rigid, move as one
21 Structure solution Watch out for… If provided, don’t assume atomic assignments are correct.Look for expected geometry, e.g. rings, octahedraMight get messy q-peaks and need to trim back to your structure.Don’t assume that if you can’t see your compound that is isn’t there and just obscured by noisy peaksIncorrect atomic assignment and missing atoms will affect the calculated phases and may mean some atoms don’t appear at first.Be patientTry any and all structure solution programs you can findDifferent programs produce different results even using the same method.Those mentioned are not the only ones but should be sufficient.
22 Structure Solution example Data taken from Oxford primer:Crystal structure determinationWilliam Clegg
23 Refinement Iterative process Be patient Sometimes it takes a long time and is difficultSometimes it is easy and quickYou must model all electron density (q-peaks) or be able to explain why modelling some peaks is not appropriate.Structure must be chemically reasonablePay attention toGeometryR-factorsQ-peaksADP’sContacts
24 Typical Refinement START Switch current atoms to anisotropic No All atomsanisotropic?YesWeightingschemeconvergedFINISH!Initial solutionNonenot convergedAll atoms correctly identified?YesModelcomplete?YesRefine… Problems?yesLargeQ-PeaksMissedAtoms?yesNoNoOdd sized orShaped ADP’sDisorder?FourierdifferencemapCheck atomicassignmentsSwitch unusual atom(s) to isotropic refinementWrong atomtype(s)?
25 * Workshops on these will be given later RefinementCommon problemsWrongly assigned atomsDisorder, particularly solvent*Twinning*Incorrect space groupQ-Peaks due to strong absorption (heavy metals present)Not all refinements will end happilyYou may have to leave some atoms isotropicYou may be unable to find or place hydrogen atomsYou may have a high R-factorYou may simply not be able to finish due to the above issues or poor quality data* Workshops on these will be given later
26 Shelx Anatomy of a shelx file TITL SAMPLE in Pbca CELLZERRLATT 1SYMM 0.5-X, -Y, 0.5+ZSYMM -X, 0.5+Y, 0.5-ZSYMM 0.5+X, 0.5-Y, -ZSFAC C H N OUNITTEMP -123L.S. 4BOND $HFMAP 2ACTACONFPLAN 20WGHTFVARO =C =OCHKLF 4REM HL9005 in PbcaREM R1 = for Fo > 4sig(Fo) and for all dataREM parameters refined using restraintsENDWGHTREM Highest difference peak , deepest hole , 1-sigma levelQQQQQQAnatomy of a shelx file
27 Common Shelx Commands L.S. Full least squares refinement. Number of cycles given after a space, e.g. L.S. 4 will give 4 refinement cyclesCGLSConjugate gradient least squares. Use for faster refinement with very large structures but only during initial refinement. You must switch to L.S. before generating a cif.FMAPFollowed by a number requests a Fourier map. Normally you will use FMAP 2, for a difference mapPLANThe number of peaks to be returned from the difference map, e.g. PLAN 20 gives 20 peaks.BONDPut Bonds into the cif file, always use BOND $HACTAA cif will be generatedWGHTThis is the weighting scheme which will be usedFVARFree variables, the first is the overall scale factor. Others may be used for various purposesSADISame distance restraint, e.g. SADI C1 C2 C3 C4 instructs the program to restrain the C1…C2 distance to be similar to the C3…C4 distanceSAMEGenerates similarity restraints for extended geometriesDFIXDistance restraint e.g. DFIX 1.54 C1 C2 puts a restraint on the C1…C2 distance to be 1.54 angstromsSIMUSimilar thermal parameters will be applied to all atoms in the list followingDELUVibration restraint. The two atoms will be restrained to have similar motion along the direction of the bondAFIXConstraints. Many types availableHFIXAdd hydrogen atoms, many options available for different hydrogen environments
29 Restraints and constraints A restraint allows a parameter to refine within limitsE.g. like applying a springA constraint fixes a parameter. It is not allowed to refine.E.g. like applying ropeRestraints are treated as additional observationsRestraints have an associated e.s.d. i.e. a measure of how strict the restraint should beMost commands have reasonable defaultsUse to correct poor geometry with chemical knowledgeCan use temporarily to maintain reasonable geometry when identifying a problem, e.g. disorderOnly use when necessary ensure e.g. distance restraints use an appropriate value, e.g. taken from CSD dataMake sure there isn’t an underlying problem before resorting to R&CMore on these in disorder workshop.
30 Atomic assignment problems Models are a picture of electron densityDifferent elements have different numbers of electronsIncorrect assignments should show up in thermal parameters.Too small an element will cause the ADP to shrinkToo large an element will cause it to growWhy?
31 Atomic assignment problems Atom is actually a nitrogen which has higher z and therefore e- density than our modelled carbon. Therefore the carbon ‘shrinks’ to increase its e- densityAtom is actually a carbon which has lower e- density than our model. Therefore thenitrogen ‘grows’ to spread out its e- density
32 Hydrogen atoms Difficult to find Incorrectly located Only one electron to diffract fromHeavier elements further obscure hydrogen positionsIncorrectly locatedDiffract from electrons not nuclei!!!Valence electron only, located ‘in bond’
33 Hydrogen placement Find them if you can Geometric placement They may often be visible in a difference mapYou may then be able to refine, partially refine them or constrain them.Geometric placementUses expected (e.g. tetrahedral) angles and distances appropriate for x-ray diffractionHFIX mnm specifies how to place e.g. tetrahedral anglesn specifies how to refine, e.g. full coords or riding
35 Some Quality indicators The conventional R-factor<10% is publishable<5% is goodGoofGoodness of fitShould be as close to 1 as possibleMore than around 0.4 away is cause for concernRintAn R-factor for data merging of equivalent reflectionsIf perfect would be 0A rough guide is to expect R1 to be close to this valueMax ShiftThe max shift of all parameters from non-linear least squares refinementShould be zero for a properly converged, finished model.
36 Finishing off Confident the structure is ok? Platon checkcif IUCr web toolPlatonDoes additional checks if FCF file is presentMake sure it is up to date!