Structure Solution and Basic Refinement

Recommended software

• Shelx– http://shelx.uni-ac.gwdg.de/SHELX/

• WinGX– http://www.chem.gla.ac.uk/~louis/software/wingx/

• Platon– http://www.chem.gla.ac.uk/~louis/software/platon/

• Solution programs (see later)• A good text editor

– e.g. Notepad++• http://notepad-plus.sourceforge.net/uk/site.htm

Chemistry Facilities

• Bruker Smart Apex CCD Diffractometer

Chemistry Facilities

From crystal to cif

• Get crystal• Short experiment to index• Long experiment to collect complete data• Integration• Absorption correction• Identify space group• Solve You start here• Refine• Cif

What is crystallography all about

• A crystal is a 3D periodic array of molecules• X-rays interact with (diffract from) electrons• Diffraction results in a regular pattern of spots

(due to constructive and destructive interference)

• Intensities observed are related to atom types and positions

• We build a model and compare the calculated diffraction pattern with the observed

The experiment

What you will get from us

• 2 or 3 files– ins file

• The shelx instruction file contains unit cell, radiation wavelength, temperature, crystal system and space group information, unit cell contents from user input

– hkl file• The reflection data, contains indexed intensities

with associated estimated standard deviations

– cif file• Contains some experimental details (not essential)

Files – ins file

TITL pg24 in P-1CELL 0.71073 10.724 12.440 12.643 72.40 79.36 73.33ZERR 2.00 0.004 0.005 0.005 0.02 0.02 0.02LATT 1SFAC C H N S HGUNIT 52 106 2 6 2PATTHKLF 4END

Files – hkl file -12 0 1 64.46 2.70 -12 -1 2 47.71 3.70 -12 -1 1 41.90 3.48 -12 -2 1 15.71 0.80 -12 -2 2 41.02 1.56 -12 -3 2 20.34 0.97 -12 -3 1 2.96 0.62 -12 -4 1 27.33 1.27 -12 -4 2 21.33 1.05 -12 -5 1 60.67 2.48 -12 -6 1 66.61 2.61 -11 -8 2 9.18 0.73 -11 -8 1 37.45 1.50 -11 -7 1 3.94 0.59 -11 -7 2 92.96 4.46 -11 -7 3 46.55 2.36 -11 -6 3 16.54 0.86 -11 -6 2 135.97 3.44 -11 -6 1 9.06 0.72

Structure Solution

• We need to get an initial model from which to work– This is called structure solution– We 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.

Structure solution

• Direct methods– Requirements

• It is desirable but not required to have a centrosymmetric structure.

– How it works• Uses 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.

Structure solution

• Direct Methods Programs– xs from the shelx suite (works for me 99% of the time)

• Instruction is TREF– You may specify a number after TREF to increase the number

of trials for difficult structures.

– Sir software• Several versions

– Sir92, Sir97, Sir2002, Sir2004– May get different results with different versions

» Variety of options for structures of different size/difficulty OR

» Can be set up through, e.g. WinGX for simplicity but less control.

Structure solution

• Patterson Methods– Requirements

• A heavy element, e.g. Fe, Cl, S, etc

– How it works• Generates a map of ‘peaks’ representing difference vectors,

i.e. interatomic vectors• Peak 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

Structure Solution

• Patterson Methods Programs– xs from the shelx suite

• Instruction is PATT• You will only get heavy atom positions back

– Dirdif• Will attempt to complete the model and guess

atomic assignments.– Can be extremely useful for complicated metal clusters,

etc.

Structure Solution

• Partial Structure Expansion– Requirements

• Knowledge of expected substructures and their geometries, e.g. a benzene ring

– How it works• Uses 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 for• Not 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.

Structure Solution

• Partial structure expansion programs– PATSEE from the wingx suite

• You must provide a list of coordinates for your substructure.

– Dirdif• Provides a small database of common geometries

e.g. benzene rings, indoles or can use your own.– Not necessarily user friendly in my opinion

Structure solution

• Charge flipping– Requirements

• Complete data (at the moment)

– How it works• Use 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

Structure solution

• Charge-flipping software– Superflip

• From originators of the method• Available as standalone (not recommended), via

WinGX, via crystals

– Flipper• Available in Platon

Structure solution

• Has it solved?– Use your chemical knowledge…– How atoms interact

• E.g. expected bond distances and angles for particular arrangements

• Reactions or decompositions which may occur• Non-bonded interaction lengths and types

– E.g. +ve to +ve is not going to be common– Charge

• Should always be neutral for a unit cell• Assignment of charge on metals, ligands

– Likely patterns of motion• E.g. neighbouring atoms are likely to have similar thermal motion• Spinning or wagging of certain groups may be expected• Groups which are likely to be rigid, move as one

Structure solution

• Watch out for…– If provided, don’t assume atomic assignments are correct.– Look for expected geometry, e.g. rings, octahedra– Might 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 peaks

– Incorrect atomic assignment and missing atoms will affect the calculated phases and may mean some atoms don’t appear at first.

• Be patient

– Try any and all structure solution programs you can find• Different programs produce different results even using the same

method.• Those mentioned are not the only ones but should be sufficient.

Structure Solution example

• Data taken from Oxford primer:– Crystal structure determination

• William Clegg

Refinement

• Iterative process– Be patient

• Sometimes it takes a long time and is difficult• Sometimes it is easy and quick

– You must model all electron density (q-peaks) or be able to explain why modelling some peaks is not appropriate.

– Structure must be chemically reasonable• Pay attention to

– Geometry– R-factors– Q-peaks– ADP’s– Contacts

Typical Refinement

Initial solution

Check atomicassignments

Refine… Problems?

Fourier difference

map

All atoms correctly

identified?

No

Yes Model complete?

No

Yes

Odd sized or Shaped ADP’s

LargeQ-Peaks

Weightingscheme

None

Wrong atomtype(s)?

Disorder?

MissedAtoms?

All atomsanisotropic?

Switch currentatoms to

anisotropic

No

Switch unusual atom(s) to isotropic

refinement

FINISH!

STARTconverged

not converged

yes

yes

Yes

Refinement

• Common problems– Wrongly assigned atoms– Disorder, particularly solvent*– Twinning*– Incorrect space group– Q-Peaks due to strong absorption (heavy metals present)

• Not all refinements will end happily– You may have to leave some atoms isotropic– You may be unable to find or place hydrogen atoms– You may have a high R-factor– You may simply not be able to finish due to the above issues or

poor quality data

* Workshops on these will be given later

Shelx

• Anatomy of a shelx file

TITL SAMPLE in PbcaCELL 0.71073 10.7308 16.4002 18.9778 90.000 90.000 90.000ZERR 8.00 0.0005 0.0007 0.0008 0.000 0.000 0.000LATT 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 OUNIT 160 152 8 32TEMP -123L.S. 4BOND $HFMAP 2ACTACONFPLAN 20WGHT 0.040400 1.691300FVAR 0.13360O1 4 1.183095 0.526967 0.621173 11.00000 0.04325 0.03499 = 0.02675 -0.00293 -0.00093 -0.01115C2 1 1.183370 0.488078 0.567136 11.00000 0.02854 0.02571 = 0.02494 0.00436 -0.00205 -0.00215O3 4 1.266176 0.500831 0.515249 11.00000 0.03273 C4 1 1.239322 0.447764 0.456425 11.00000 0.03222

HKLF 4 REM HL9005 in PbcaREM R1 = 0.0452 for 3267 Fo > 4sig(Fo) and 0.0476 for all 3421 dataREM 226 parameters refined using 0 restraints END WGHT 0.0404 1.6913 REM Highest difference peak 0.267, deepest hole -0.198, 1-sigma level 0.039Q1 1 0.8842 0.3387 0.6174 11.00000 0.05 0.27Q2 1 0.9964 0.3517 0.6038 11.00000 0.05 0.24Q3 1 0.9221 0.3187 0.5592 11.00000 0.05 0.23Q4 1 0.6446 0.2208 0.7061 11.00000 0.05 0.22Q5 1 0.9203 0.3060 0.4928 11.00000 0.05 0.21Q6 1 0.9370 0.3938 0.5769 11.00000 0.05 0.20

Common Shelx CommandsL.S. Full least squares refinement. Number of cycles given after a space, e.g. L.S. 4 will give 4

refinement cycles

CGLS Conjugate 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.

FMAP Followed by a number requests a Fourier map. Normally you will use FMAP 2, for a difference map

PLAN The number of peaks to be returned from the difference map, e.g. PLAN 20 gives 20 peaks.

BOND Put Bonds into the cif file, always use BOND $H

ACTA A cif will be generated

WGHT This is the weighting scheme which will be used

FVAR Free variables, the first is the overall scale factor. Others may be used for various purposes

SADI Same 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 distance

SAME Generates similarity restraints for extended geometries

DFIX Distance restraint e.g. DFIX 1.54 C1 C2 puts a restraint on the C1…C2 distance to be 1.54 angstroms

SIMU Similar thermal parameters will be applied to all atoms in the list following

DELU Vibration restraint. The two atoms will be restrained to have similar motion along the direction of the bond

AFIX Constraints. Many types available

HFIX Add hydrogen atoms, many options available for different hydrogen environments

Back to our example…

Restraints and constraints• A restraint allows a parameter to refine within limits

– E.g. like applying a spring• A constraint fixes a parameter. It is not allowed to refine.

– E.g. like applying rope• Restraints are treated as additional observations• Restraints have an associated e.s.d. i.e. a measure of how strict the

restraint should be– Most commands have reasonable defaults

• Use to correct poor geometry with chemical knowledge• Can use temporarily to maintain reasonable geometry when

identifying a problem, e.g. disorder• Only use when necessary ensure e.g. distance restraints use an

appropriate value, e.g. taken from CSD data• Make sure there isn’t an underlying problem before resorting to R&C• More on these in disorder workshop.

Atomic assignment problems

• Models are a picture of electron density– Different elements have different numbers of

electrons– Incorrect assignments should show up in

thermal parameters.– Too small an element will cause the ADP to

shrink– Too large an element will cause it to grow– Why?

Atomic assignment problemsAtom is actually a nitrogen which has higher z and therefore e- density than our modelled carbon. Therefore the carbon ‘shrinks’ to increase its e- density

Atom is actually a carbon which has lower e- density than our model. Therefore thenitrogen ‘grows’ to spread out its e- density

Hydrogen atoms

• Difficult to find– Only one electron to diffract from– Heavier elements further obscure hydrogen

positions

• Incorrectly located– Diffract from electrons not nuclei!!!– Valence electron only, located ‘in bond’

Hydrogen placement

• Find them if you can– They may often be visible in a difference map– You may then be able to refine, partially refine

them or constrain them.

• Geometric placement– Uses expected (e.g. tetrahedral) angles and

distances appropriate for x-ray diffraction– HFIX mn

• m specifies how to place e.g. tetrahedral angles• n specifies how to refine, e.g. full coords or riding

Hydrogen Placement

• Common HFIX types

1 2 3

4 8

Some Quality indicators• R1

– The conventional R-factor– <10% is publishable– <5% is good

• Goof– Goodness of fit– Should be as close to 1 as possible

• More than around 0.4 away is cause for concern

• Rint – An R-factor for data merging of equivalent reflections– If perfect would be 0– A rough guide is to expect R1 to be close to this value

• Max Shift– The max shift of all parameters from non-linear least squares refinement– Should be zero for a properly converged, finished model.

Finishing off

• Confident the structure is ok?

• Platon checkcif– IUCr web tool

• http://checkcif.iucr.org/

– Platon• Does additional checks if FCF file is present• Make sure it is up to date!