Synchrotron radiation for single crystal
diffraction

Single Crystal Diffraction
Synchrotron
yapplications
pp
Cheiron School, Spring8, 2012Claire Wilson

Intensity Formula for Diffracted Xrays• Ihkl = Io (λ3 /ω) (Vx L p A/V2) |Fhkl|2– Io ‐ incident beam intensityy– Vx volume of crystal– λ3 ‐ increase λ 2x ‐ increase scattering 8x– |Fhkl|2 depends on unit cell contents – atomic
scattering
i ffactor• ω = rotation velocity of the crystal; L = Lorentz; p = the polarization
factor; A = absorption factor ; V = volume of the unit cell

• SomeSproperties
i off synchrotron
hradiation
di i very
valuable to single crystal diffraction– Very intense xray beam
– Tunable wavelength– Broad energy spectrum– Pulsed structure• Improve quality of some ‘standard’ studies• Provides opportunities
ppfor studies andapplications not possible with laboratory xraysources

Small weakly diffracting crystals• Use– very high intensity of synchrotron radiation– Focussed small beams– Longer wavelength xrays (tunability)• Study crystals 10s microns (and smaller)• Standard
S d d experimentibutb many excitingii
and scientifically important structures
not possible using laboratory sources

Crystal size
Typically for synchrotron
single diffraction studies
looking at crystals 10‐100
microns in size
1μm= 1x10‐6m=10,000Å
m=10 000Å

Cave full of ggiant crystals
yof gypsum
gypin Mexico some as long as 11 metres!

Rapid data collection ‐ automation• Short data collections –sample changing
becomes significant partof beamtime• Robotic Sample Changer

LLeighi h ett al,l Nature
N tChChem. 4,
4 15‐20
15 20 (2012)
http://www.catenane.net/home/knot_paper_2011.html– Improved efficiency ofscreening samples– Reduce number and timespent on searches– Return to original crystal

High pressure studies

High pressure studies• Experimental challenges• Look at effect of pressure on structure– Diffraction data limited – shaded by pressure cell bodythat block xrays from sample or detector (40° cone)– High absorption by cell
– Crystals relatively small– New polymorphs
p yp– New intermolecular interactions– Phase transitions• Synchrotron radiation advantages– High xray flux – small crystals, improve statistics– ShortSh wavelengthlh ((tunability)bili ) – improvei
completeness
lof data – compress diffraction pattern

Diamond Anvil example

Gas Cell

The effect of pressure on Cu‐btc :framework compression vs. guest inclusion
Detailed structural data on the effect of high pressure on Cu‐btc
Cu btc––•Application of pressure causes solvent to be squeezed into thepores until a phase transition occurs, driven by the sudden
compression and expansion of equatorial and axial Cu‐O bonds
On increasing pressure further to 5.0 GPa, we enter a poreemptyingt i region,iwithith whichhi h ththe hihighh pressure squeezes ththesolvent out of the pores; this is accomodated by the extension of
the compliant (axial) Cu‐O2 bond.

Data collected on I19 at ~0.5GPa steps from ambient pressure
to 5GPa

2.15

2.10
1.95
1.90
1.85
1 80
1.80
0

3 distinct but interconnected pore volumes in Cu-btc. Guest
accessible cavities at (0,0,0) (pink), (1/2,1/2,1/2) (yellow) and(1/4,1/4,1/4) (blue) are shown.

Advantages
g of use withsynchrotron radiation• Smaller samples
p possible
pmaximising gas penetration• Rapid data collection allows
monitoring in‐situ monitoring ofprocess and continuous evaluation• Increased intensity overcome highbackground from borosilicate glass

2 20
2.20

Cu-O bond length (Å)

•1

234

5

6

Pressure (GPa)/ , / ) (blue, ∼8.4 Å diameter), and (1/4, 1/4, 1/4) (yellow, ∼5.4 Å diameter1 2 1 2The effect of pressure on Cu‐btc: frameworkcompression vs.
vs guest inclusion
Alexander J. Graham , Jin‐Chong Tan , David R. Allanand Stephen A. Moggach
Chem. Commun., 2012,48, 1535‐1537

Cu paddlewheel units present in Cu-btc showing
the equatorial and axial Cu-O bonds, Cu-O1 andCu-O2 respectively.

Thanks to Stephen Moggach,
University of Edinburgh,UK•••

Flow cell – used to flow a gas or put crystal under vacuum
Crystals can be evacuated first with vacuum, in conjunction
with heatingg from the Cryostream,y, then ggases appliedpptosample
Gases that can be used N2, H2, Ar, Kr, SO2, CO2, CO, Ne, HCl,
H2S, NO

Gas Cell example•SampleSample initially activated under vacuum
vacuum,• collecting data as heated from 283 to 400K
•Monitoring MeOH content until total desolvation ~22hrs•Cell loaded with CO2, e‐ρ monitored•CO2 removed under vacuum•SO2 loaded into environmental ggas cell
•Increase in e‐ρ – location of 2 S‐atom sites

Zn2(ox)(atz)2]·2MeOH (ox = oxalate,atz = 3-amino-1,2,4-triazolate)desolvation

CO2
adsorption

SO2
adsorptiondesorptiondesorpt
ion

Crystalystructure off [Zn[ 2((ox)(atz))( )2]]∙0.42SO2, indicating
gthe sulfur positions within the pores

Thanks to Anna Warren, I19

Spring‐8 BL02B1 – short wavelength,
high resolution, high quality data

Charge density studies• Similar
Si il experiment
it – muchh more information
i fti• Extend conventional spherical atom model toexplore electron density – bonding effects,effects
electronic structure and properties• More complicatedpmodel, manyy moreparameters and relatively small effect• Need accurate, highly redundant, highresolution data including weak reflections• Short wavelength, high intensity, high quality
beam – increase resolution
resolution, reduce systematicerrors, measure weak reflections accurately
P. Coppens, B.B. Iversen & F.K. Larsen, Coord. Chem. Rev., 249, 179‐195,2005
use of synchrotron radiation for charge density studies

Anomalous scattering• Closelto absorption
bi edge
dscattering factor no longer
wavelength independent• f = f0 + f’ + if”– f0 scattering of unperturbed atom,f’ + if” real and imaginarygyp
parts ofanomalous scattering• Magnitudes of f’
f and f”
f canchange by several electrons

MADAnomalous scattering• Multiwavelength Anomalous Diffraction• An approach to solving the phase probleminprotein structure by comparing structure
factors collected at different wavelengths
wavelengths,
including the absorption edge of a heavy‐atomscatterer.

• Elementlandd valencelspecific
ifi diffdiffractioni• identify and locate different elements even on
same site e.g. Fe and Co or Fe(II)/Fe(III),
Gd(I)/Gd(III), Eu(II)/Eu(III)• Edge differ 2‐6eV for increase of 1 in oxidationstate• Use data collected at several wavelengths aroundabsorptionpedge
g and refine f’ at each site to
identify valence state• W. Hendrickson (Hendrickson, W. A., 1991, Determination ofmacromolecularl l structures fromfanomalousl
diffraction
ff
off
synchrotron radiation. Science, 254, 51–58.)

Multitemperature Resonance‐Diffraction and Structural Study of the Mixed‐Valence Complex
p [[Fe3O(OOCC(CH(( 3)3)6((C5H5N))3]
Multi‐temperature structural data showed valence trapping tooccur on coolingcooling.
Room temperature have 2/3 of sites with intermediate
geometry between Fe(II) and Fe(III)At low temperature 2 x Fe(III) and 1 x Fe(II)Data collected at 13 energies and 4 temperatures and f’ ateach of the Fe sites refined for each case
Determine absorption edge position for each site at eachtemperature

Wu et al, Inorg. Chem. 1998, 37, 6078‐6083•

Review by Madeleine Helliwell, J. Synchrotron Rad (2000), 7, 139‐147

Photocrystallography• Use single crystal diffraction to investigate
g induced byy lightg
structural changes• Light of appropriate wavelength excite
electron to excited states• change in electron distribution – atomic
displacements and sometimes
photoisomerism or solid
solid‐state
state reaction

Photocrystallography

Metastable excited states

Range of timescales• Irreversible – standard experimentp
before andafter structure• Metastable – excited state long lived as long as
environment retained – e.g. Low temperature• Microsecond and shorter lived species – time
resolved studies• Metastable
bl – excited
i d state llong lilived
d as llong as
environment retained – e.g. Low temperature• Typically partial conversion ~20% ‐ ‘disordered’structure with ground state• Experimental steps – collect ground state
structure (in dark at low temperature) – irradiate– collect activated structure (mix of ground stateand metastable state)• Advantage with synchrotron radiation – small
crystalyand rapid
p data collection••

Feature article J.M. Cole Acta Cryst. (2008). A64, 259–271
And tutorial review in Analyst, 2011, 136, 448‐455

Metastable ‐ photoisomerism• First complex studied by photocrystallographic techniques
Na2[Fe(CN)5(NO)] ‐ 2 photoactivated metastable complexes ‐linkage isomers of the ‘‘ground state’’ nitrosyl complex
Coppens et al,al J.
J Am
Am. Chem
Chem. Soc.,
Soc 119,119 2669 (1997).
(1997)• [Ru(NH3)4(H2O)(1‐SO2)][tosylate]2 studied by Coppens et al andground state and one metastable state determined, 2nd metastablestructure determined by Raithby et al
Coppens et al Inorg. Chem., 124, 9241 (2002 and Inorg. Chem., 42, 140 (2003). P.R. Raithby
et al, Chem. Comm., 2448 (2006).

Short‐lived species – time resolvedstudies• MicrosecondMid lifetimes
lif ti‐ reversibleibl on shorth t titimescalel• use stroboscopic (optical)pump‐(xray)probe techniques• Laser pump excited state and probe excited structurewith synchronised xray probe very short delay afterplaser pulse• Need synchrotron radiation – sufficient photos perchopper cycle where chopper pulse of photons• Limited time resolution with monochromatic beam –throwing many photons away

Coppens et al Acta Cryst A66, 179‐188, 2010

Picosecond lifetimes – Laue method

Laue Method• Polychromaticl hi experiments
iusingi llarger
bandwidths increase flux by 1000x or morecomparedd tot monochromatic
hti bbeam• Collect data with a single synchrotron pulse.
• Laser pulse followed by single X‐ray pulse ‐ timeresolution determined by the largest width of thepump and the probe pulses.
• With femtosecond lasers time resolution
determined by width of synchrotron pulse,
typicallyyp
y 50–160 p
ps, dependingp
g on fill ppattern• Stationaryi
crystall• White ((or ppink)) beam – ppolychromaticy• Very fast shutter• Simple experimental set up but much more
complicated data processing – wavelength
dependent effects• Wavelength normalisation – different incident
intensity, sample diffracting power anddetector response

Laue Method
Considerable
C
id bl workk tot improvei
accuracy andd quality
litof time resolved studies using Laue techniques• The development of Laue techniques for single‐
singlepulse diffraction of chemical complexes– [Coppens et al Acta Cryst. (2011). A67, 319
319–326]
326]

Simulation of Laue diffraction pattern for a lanthanum complex with spots
colour‐coded for wavelength. Short wavelengths in blue and then throughthe rainbow colours to red at the longest wavelengths. Actual wavelength
bandpass used in this simulation is 0.5–1.5 Å.
M. Harding, Acta Crvst. (1995). B51,432‐446• Time‐resolved Laue diffraction of excited species
at atomic resolution:l
100 ps single‐pulselldiffraction of the excited state of theorganometallic complex Rh2(μ‐PNP)(μ PNP)2(PNP)2∙BPh4– [Coppens et al Chem. Commun., 2011, 47, 1704‐1706]

A TimeTime‐resolved
resolved X‐ray
X ray Beamline

Future• htt
http://pfwww.kek.jp/adachis/NW14/NW14.htm// fk k j / d hi /NW14/NW14 ht•NW14A is an insertion device beamline aimingg for time‐
resolved X‐ray diffraction, scattering and absorption
experiments. This beamline is particularly suitable forstudying ultrafast dynamics in condensed matter systems
such as organic and inorganic crystals, biological systems,
liquids etc. Structural dynamics triggered by optical laser
pulses is captured with the synchronized pump
pump‐and‐probe
and probesystem. With the relatively large amount of X‐ray photon
flux derived from the undulators, it is possible to produce
atomic‐scalet il movies
i off theth photo‐induced
h t i d d phenomena
hwith
ith
100‐ps resolution.
• J. Synchrotron
yRad. (2007).
() 14,, 313–319

Much shorter lifetimes studied using the XFEL?