a quick guide to crystallography and crystal growth ross harrington
TRANSCRIPT
![Page 1: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/1.jpg)
A quick guide to crystallography and crystal growth
Ross Harrington
![Page 2: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/2.jpg)
Outline
What is crystallography?
How it works and why you need good crystals
The data collection procedureWhere the pitfalls lie.
What are crystals? Crystal growth Factors that affect diffraction quality National Service and Diamond
![Page 3: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/3.jpg)
Books
![Page 4: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/4.jpg)
What is crystallography?
Determining the 3-D structure of a molecule
Provides relationship of structure to physical and chemical properties
Meaning of ‘structure’: relative positions of atoms in a molecular or other
material, hence complete geometrical description: bond lengths and angles molecular conformation absolute configuration, etc.
![Page 5: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/5.jpg)
Absolute Configuration
The ‘absolute structure’ defines the configuration of the chiral centres in a molecule that is chirally pure (i.e. R or S).
In this case molecules will crystallise in a chiral space group i.e. One with no centre of symmetry (mirror or inversion centre)
Can not apply to racemic mixtures or molecules that contain internal symmetry
![Page 6: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/6.jpg)
What is crystallography?
Not a spectroscopic technique
All parts of the diffraction pattern contribute to all parts of the structure
So- all parts of the structure also contribute to all parts of the diffraction pattern.
![Page 7: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/7.jpg)
The two techniques
Spectroscopy
UV, light, IR, etc.
Crystallography
X-rays (or neutrons)Usually monochrmoatic
Sample
detector: measure the variation of intensity with changing λ in one direction
Crystal
detector: measure the variation of intensity with direction for one λ (a diffraction pattern)
![Page 8: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/8.jpg)
Diffraction
X-rays interact with the electrons surrounding the nuclei (and in the bonds)
So the heavier the atom, the more electrons are present, so diffraction is more intense.
Diffraction is proportional to the number of electrons present
Diffraction drops off at higher angle of incidence (theta)
So locating H atoms is difficult
![Page 9: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/9.jpg)
Other points of note
Each spot in a diffraction pattern is one data point (h,k,l).
The number of data points possible is proportional to the size of the unit cell
The size of the unit cell is proportional to the size of the molecule being analysed.
So bigger molecules take longer to obtain data.
![Page 10: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/10.jpg)
What is a crystal?
A solid material with infinite order in three dimensions
Therefore all molecules are in exactly the same relative environment
This means that translational and possibly other symmetry is present
These are:
Inversion centres, rotation axes and mirrors
![Page 11: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/11.jpg)
Defining a unit cell
![Page 12: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/12.jpg)
The Process
![Page 13: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/13.jpg)
The Experiment
Grow Crystals
Select Crystal
Collect/process data
Solve and refine structure
Publish/Patent
![Page 14: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/14.jpg)
Grow good crystals
Garbage in = Garbage out
Relatively large See-through/clear Single Not amorphous
![Page 15: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/15.jpg)
1. Grow good crystals
![Page 16: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/16.jpg)
![Page 17: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/17.jpg)
![Page 18: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/18.jpg)
![Page 19: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/19.jpg)
![Page 20: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/20.jpg)
![Page 21: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/21.jpg)
![Page 22: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/22.jpg)
![Page 23: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/23.jpg)
![Page 24: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/24.jpg)
![Page 25: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/25.jpg)
General principles of crystal growth
It isn’t the same as recrystallisation Crystals grow in a settled environment Solvents make a big difference- both purity
and volatility Solubility is important Seeding can work The first try isn’t always the best Take Time....
![Page 26: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/26.jpg)
Choose your vessel carefully
Crystals need to be removed easily Don’t use huge vessels with small volumes Try to avoid vessels with very small
apertures Try to avoid vessels with wide shoulders Avoid very smooth or very scratched
vessels
![Page 27: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/27.jpg)
My least favourite
![Page 28: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/28.jpg)
Crystal Growth: Solution methods
General principles
Choose your solvents carefully- ‘like dissolves like’
Anti-solvents can be added to reduce solubility
Varying concentrations of the two can give the best conditions for crystallisation
![Page 29: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/29.jpg)
Crystal Growth: Concentration
Essentially ‘slow evaporation’ If using mixed solvents, the better solvent
should be most volatile. Rate of evaporation can be controlled:
Temperature Gas flow Aperture size
Note: Avoid hazards such as build up solvent in confined spaces.
Keep an eye on the sample.
![Page 30: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/30.jpg)
Examples
NMR tubes left in back of Fume Cupboard
![Page 31: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/31.jpg)
![Page 32: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/32.jpg)
Crystal Growth: Slow cooling
Two methods: Allow a hot, almost saturated solution to cool
slowly to room temperature Cool a similar solution made up at RT, using
a fridge or freezer
Cooling time can be manipulated
![Page 33: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/33.jpg)
Examples
![Page 34: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/34.jpg)
Crystal Growth:Solvent diffusion
Essentially two almost immiscible solvents layered on top of each other
The poorer solvent mixes with the better solvent and causes crystallisation
Can also use specialist apparatus such as H-cells
![Page 35: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/35.jpg)
Examples
![Page 36: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/36.jpg)
Crystal Growth: Vapour Diffusion
Relies on solvent/antisolvent principle again One sample tube inside another Volatile anti-solvent diffuses into solution via
the vapour phase This reduces solubility and hence
crystallisation occurs.
![Page 37: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/37.jpg)
Examples
![Page 38: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/38.jpg)
Crystal Growth: Exotic methods
Sublimation Convection In situ crystallisation Reactant diffusion Solid synthesis (grinding) Solvothermal (temp and pressure)
![Page 39: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/39.jpg)
![Page 40: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/40.jpg)
When you get crystals
DO NOT filter them DO NOT put them under vacuum DO NOT let them dry out DO leave them in the same environment DO reduce the solvent level slightly DO give us as many crystals as possible
![Page 41: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/41.jpg)
Re-growing crystals
Tend not to say ‘recrystallise’ SD example CH2Cl2 vs CHCl3
![Page 42: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/42.jpg)
Re-growing crystals
R1 = 0.0210, wR2 = 0.0544Largest peak and hole 0.87 and 0.54 e Å3
![Page 43: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/43.jpg)
Collecting the data
Choosing the crystal (up to 15 minutes) Collecting initial images (10 minutes) Checking against known cell (5 minutes) Data collection (30 minutes to 3 days) Processing data (20 minutes) Solving and refining structure (30 minutes to
a week) Publishing structure (up to 15 years)
![Page 44: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/44.jpg)
What I am aiming for
Good enough to get a structure? Resolution limits (0.84Å Mo, 0.9Å Cu)? Publishable in Acta?
‘The best possible data you can get from the sample you have’
![Page 45: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/45.jpg)
‘Data out’
As high a resolution as possible
High redundancy on all reflections (at least 2)
Good statistics (Rsigma, Rint) on whole data set
Low residual peaks in the difference map
A good R factor
![Page 46: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/46.jpg)
Good and bad patterns
![Page 47: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/47.jpg)
Good and bad patterns
![Page 48: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/48.jpg)
Effect of disorder ?
R1 = 0.0437, wR2 = 0.0938Largest diff. peak and hole 0.43 and 0.27 e Å3
![Page 49: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/49.jpg)
Effect of disorder ?
R1 = 0.0562, wR2 = 0.1196Largest diff. peak and hole 0.96 and 0.40 e Å3
![Page 50: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/50.jpg)
Twinning
Twinning occurs where the unit cell has symmetry elements that the contents of the cell do not
Example: A Monoclinic structure with β close to 90o
Two types of Twinning Merohedral: occurs where lattice system has
two point groups Non-merohedral: imperfect overlap of
diffraction from two components
![Page 51: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/51.jpg)
Consequences of twinning
![Page 52: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/52.jpg)
Consequences of twinning
![Page 53: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/53.jpg)
Pros and cons of crystallography
Pros Relatively quick Unambiguous Loads of info Picture tells a thousand
words
Cons You have to grow crystals Selected crystal may not
be representative Solid state may be
different from solution Not useful for elemental
analysis
You will need supporting evidence for analysis of the bulk sample e.g. Powder diffraction
![Page 54: A quick guide to crystallography and crystal growth Ross Harrington](https://reader038.vdocuments.site/reader038/viewer/2022102908/56649e4d5503460f94b433f0/html5/thumbnails/54.jpg)
When all else fails...
Use a stronger X-ray source We have access to:
The National Service (rotating anodes and mirrors) ~15 samples in 6 months
Diamond Light Source (synchrotron)
~ 4 days every 6 months