High-Pressure Crystallography
Francesca P. A. Fabbiani
Emmy-Noether Jr. Research Group
Welcome
Part 1
•
Introduction to high-pressure
research
•
Experimental setup
Dr. Michael Ruf
Product Manager, SC-XRD
Madison, WI, USA
Dr. Francesca P. A. Fabbiani
 High-pressure crystallography with
emphasis on single-crystal X-ray
structure determination
 High-pressure crystallization
 Solid-state polymorphism
 Molecular compounds with
emphasis on pharmaceuticals and
biomolecules
Part 2
•
Collecting high-pressure data,
solving and refining structures
•
Molecular organic
materials, single crystals
Introduction to
High-Pressure Research
High-Pressure Research
Range of pressures and temperatures now accessible
with static compression techniques in the laboratory.
•
Planetary science and physics (e.g.
minerals, perovskites, clathrates,
ices – N.B. 15 polymorphs of H2O
to date!)
•
Synthesis of novel materials (e.g.
superhard materials, nanoporous
materials, MOFs)
Mao H , Hemley R J PNAS 2007;104:9114-9115
©2007 by National Academy of Sciences
•
Chemistry/molecular compounds
(e.g. amino acids, molecular
magnets, pharmaceuticals)
•
Proteins, pressure-induced
denaturation, folding
Phase diagram of water
Source: Martin Chaplin, http://www.lsbu.ac.uk/water/phase.html
High-Pressure Research
Cubic BN
•
Industrial applications, e.g.
pressure treatment of food
•
Origin of life/ sustained life at the
bottom of the oceans
Source: Wikimedia Commons
•
Access new materials, probe
intermolecular interactions
•
Understand polymorphic
transformations
Beta sheet
Paracetamol
Source: Wikimedia Commons
•
Interplay with theory
Source: Wikimedia Commons
High-Pressure Scale
(1000 atmospheres ≈ 1 kbar = 100 MPa = 0.1 GPa)
Non-equilibrium
pressure of H2
Pressure
gas in
intergalactic inside a light
bulb
space
Hydrogen
becomes
metallic
Centre of the
Earth
Peak pressure
of fist on
Ice skater
concrete
standing
on ice during karate
strike
Centre of
the Sun
GPa
10-36
10-16 10-5 10-4 10-2 10-1
1
10
102 103 104
Greatest
Graphite
Sea level
Earth
depth in
becomes
atmosphere at
oceans
diamond
altitude of 300
miles
Molecular materials
108
Centre of
Jupiter
Orders of magnitude available for pressure variation >> temperature variation
Experimental Setup
Pressure Generation for in situ XRD:
Diamond-Anvil Cell
1958
First diamond anvil cell at NIST Gaithersburg Museum
2009
Aluminium DAC mounted on a
goniometer head
5 cm
DAC manufactured by Dr. H. Ahsbahs
F. P. A. Fabbiani et al. CrystEngComm
(2010), 12, 2354-2360
Source: G. J. Piermarini, Wikimedia Commons
Pressure Generation for in situ XRD:
Diamond-Anvil Cell
F
P= F/A (kgms-2/m2 = N/m-2 = Pa)
Tightening screws
Diamond
Ruby
Backing plate
Sample
Gasket
A
Diamond
F
Diamond
Choose your DAC carefully:
backing plates material, diamond
cut, purity and culet size, gasket
hole size, DAC opening angle
DAC Loading
•
•
•
Prepare gasket, i.e. sample chamber
Load sample together with pressure
calibrant, e.g. ruby chip
(fluorescence) or quartz single crystal
(diffraction)
Sample can be in the solid (direct
compression in an hydrostatic
medium), liquid or gas phase (in situ
crystal growth). A solution can also
be loaded for in situ crystal growth
Equipment for DAC preparation
• EDM machine (spark eroder) or
laser to drill gasket hole
• Stereomicroscope with good
magnification, large working
distance and polariser/analyser
• Small spectrometer with large
working distance to monitor ruby
fluorescence if using ruby as
pressure calibrant
DAC Loading
Three main sample loading methods available
Sample loading methods depend on:
•
Nature of the sample under investigation
•
Aim of experimental investigation
The focus here is on molecular organic materials for single-crystal
X-ray diffraction
300 µm
300 µm
“Fathers” of high-pressure research: G. H. J. A. Tammann (1861-1938), P. W. Bridgman (1882-1961)
DAC Loading
Approach 1: Direct compression in a hydrostatic medium
•
Good for studying polymorphism in small molecules
•
Less effective for studying polymorphism in larger and/or rigid molecules:
kinetic barrier associated with molecular rearrangement is usually large
•
Good for studying evolution of structure as a function of pressure, for
obtaining p-T phase diagrams and isothermal equation of states
•
Choice of hydrostatic medium: solubility/ freezing pressure considerations
DAC Loading
Approach 2: In situ crystallisation and growing from the melt
•
Excellent method for crystallising new polymorphs of compounds with
melting points < 40°C and for comparing with low-temperature structures
•
Not effective for higher melting organic compounds, which
can decompose before the onset of melting
p
L
S
V
T
DAC Loading
Approach 2: In situ crystallisation and growing from the melt
heat
cool
DAC Loading
Approach 3: In situ crystallisation from solution
•
Excellent method for crystallising new polymorphs and solvates.
No limitation to low melting point or small molecules
•
Can vary solvent, pressure, temperature and concentration
•
Prerequisite: relatively high solubility of the solute; solubility of solute
increases with increasing temperature and decreases with increasing
pressure
Outline
• Introduction to high-pressure research
• Experimental setup
Part 1
Part 2
• Collecting high-pressure data, solving and refining structures
Molecular organic materials, single crystals
Collecting high-pressure
data, solving and refining
structures
Data Collection
•
•
Centre on the diffractometer, 2-step
procedure: optical centring and direct
beam centring (Dawson et al. 2004)
or diffractometric measurements
(King & Finger 1979, Dera &
Katrusiak 1999)
Choose suitable data collection
strategy (and wavelength, if
applicable) and exposure time;
maximise no. frames per run (this
helps during data integration if
integrating with Bruker software)
A. Dawson et al. J. Appl. Cryst. (2004), 37, 410-416
H. E. King & L. W. Finger J. Appl. Cryst. (1979), 12, 374-378
P. Dera & A. Katrusiak J. Appl. Cryst. (1999), 32, 510-515
Set up @ GZG Göttingen
~ 144 mm
Short collimator and long beamstop
Diffracted beam D
ΨD
2θ
Data collection in
transmission mode
Incident beam I
Collimator
Axis of
symmetry
Data Collection
For one orientation of the DAC, the
accessible region of reciprocal space
is determined by the detector distance
and the DAC opening angle
ω
Steel support of the DAC
starting to obscure the
detector
R. J. Angel et al. Phase Transitions (1992), 39, 13-32
By a combination of ω-scans using
different orientations of the DAC in φ,
and different orientations of the
detector in 2θ, about ⅓ of all
reflections can be collected (Angel et
al. 1992). This can be increased by
collecting more data with a different
orientation of the DAC with respect to
χ (see later)
Data Collection
Example of data collection strategy for a 3-circle diffractometer, detector
distance = 7 cm and DAC perpendicular to the beam @ phi = 0°, ½ DAC
opening angle = 45°
Scan Type
2 Theta Omega Phi
Sweep Scan direction
Omega
-28
-40
0
30
+ve
Omega
28
40
0
65
-ve
Omega
-28
-220
0
65
+ve
Omega
28
-140
0
30
-ve
Omega
-28
-40
180
30
+ve
Omega
28
40
180
65
-ve
Omega
-28
-220
180
65
+ve
Omega
28
-140
180
30
-ve
Phi
0
0
60
60
+ve
Phi
0
180
60
60
+ve
Phi
0
0
150
60
+ve
Phi
0
180
150
60
+ve
Important: check hardware limits; check diffraction limits and adjust
2 Theta and Omega accordingly
Data Collection
Set up @ GZG Göttingen
X-ray Crystallography
Diffracted beam D
ΨD
2θ
Limited sampling of
reciprocal space 
data completeness
and resolution
Incident beam I
Collimator
Absorption and
shadowing
Axis of
symmetry
Sample scattering
power (and size)
Background
data collection
data processing
structure solution
structure refinement
Data Completeness
Coverage of reciprocal space
Increasing Data Completeness
Collect
Rotate by 120°
and collect
Rotate by 120°
and collect
On a 3-circle
diffractometer
•
Rotation of the DAC
•
DAC with large opening angle + non-diffracting backing plates
•
Data collection with short-wavelength radiation (see later)
•
Careful orientation of the crystal in the DAC (ambient p)
•
Multiple or twinned crystals
F. P. A. Fabbiani et al. CrystEngComm (2010), 12, 2354-2360
Data Processing
•
Data indexing identify reflections arising from sample
Harvesting reflections
If large background variations,
reduce the number of images and
runs
Choose an appropriate value
It is useful to exclude certain regions,
e.g. Be rings, gasket rings; if sample
reflections are scarce and indexing is
difficult, try omitting high-resolution
regions, where diamond reflections
are more abundant. This can also be
achieved through a reciprocal lattice
viewer (recommended)
Data Processing
•
Data indexing identify reflections arising from sample
Reciprocal lattice viewer
The reciprocal lattice
viewer is an invaluable
tool for indexing, for
assessing data quality
and for twin-spotting.
Reflections can be
conveniently assigned
to different groups and
exported for indexing
with external programs,
e.g. CELL_NOW
Data Processing
•
Data indexing identify reflections arising from sample
•
Data integration mask out regions of detector obscured by the DAC;
choose appropriate resolution; background correction
The following are recommendations based on personal
experience. There is no “one-fits-all” strategy that will work for
every sample: try different options to optimise your integration.
Once the integration parameters have been optimised, I would
strongly recommend performing successive integration cycles
(“UB matrix update”) for best intensities and unit cell parameters
Data Processing
•
Data indexing identify reflections arising from sample
•
Data integration mask out regions of detector obscured by the DAC;
choose appropriate resolution; background correction
Try to keep the box
size small. If problems
with convergence:
uncheck this option
If background is jumpy 
choose high frequency;
otherwise reduce
Twins can be easily
handled
Data Processing
•
Data indexing identify reflections arising from sample
•
Data integration mask out regions of detector obscured by the DAC;
choose appropriate resolution; background correction
This option might be useful
for synchrotron data
Threshold for strong
reflections: lower this to,
e.g. 8 for weak data
For using dynamic masks
generated with an external
program
Data Processing
Typical frames from CCD Area Detector
Diamond
reflection
Sample
reflection
Powder ring from
Beryllium
backing discs
(now almost
obsolete)
Powder ring from
steel gasket
almost invisible at
2θ = 0 (gasket and
beam size
dependent)
Dynamic mask
for integration
Shading from
DAC opening
angle
Dynamic masks: A. Dawson et al. J. Appl. Cryst. (2004), 37, 410–416; N. Casati et al. J. Appl. Cryst. (2004), 40, 620-630
Data Processing
•
Data indexing identify reflections arising from sample
•
Data integration mask out regions of detector obscured by the DAC;
choose appropriate resolution; background correction
Generate dynamic masks “on the fly”, e.g. with the Bruker SAINT integration
software, V8.07A run from the command line (“Advanced options”)
Input DAC
geometry
Data Processing
•
Data indexing identify reflections arising from sample
•
Data integration mask out regions of detector obscured by the DAC;
choose appropriate resolution; background correction
•
Scaling and absorption correction 2-stage procedure: analytical
correction for DAC components and gasket shadowing, see programs
by S. Parsons, A. Katrusiak and R. J. Angel; multiscan correction to
correct for other systematic errors and for scaling, e.g. SADABS.
Beware of outliers, e.g. diamond reflections!
•
Space group determination difficulty related to completeness,
redundancy, resolution and crystal orientation  systematic absences
are not always present
Data Processing
•
Structure solution direct methods, global optimisation methods
(borrowed from powder diffraction), molecular replacement, etc.:
numerous programs available!
•
Data merging crucial step; robust-resistant and experimental (1/σ2)
weighting scheme with SORTAV
SORTAV: R. H. Blessing J. Appl. Cryst. (1995), 30, 421–426
Refinement
•
Very high-quality high-pressure data can be collected nowadays. It is
nevertheless important to be realistic during refinement. Refinement of
ADPs for all non-H atoms might not be possible
•
Most commonly encountered problem: low data to parameter ratio;
restraints are your friends: treat them well and be generous
•
Always investigate outliers before omitting reflections: go back to the
original frames
•
The following are examples taken from my own research
CRYSTALS: P. W. Betteridge et al. J. Appl. Cryst. (2003), 36, 1487
SHELXL: G. M. Sheldrick Acta Cryst. (2008), A64, 112-122
Refinement
Example of problematic data, lab source
In situ crystallisation study
Cell setting, space group
Monoclinic, P21/n
a, b, c (Å)
7.630(2) 17.209(3) 7.3708(11)
β (°)
103.923(8)
Z
4
Multi-scan abs. correction Tmin/Tmax
0.29
No. of measured, independent and
observed [F > 4σ(F)] reflections
801, 203, 172
Rint
0.05
No. of parameters
14
R1[F > 4σ(F)], wR2(F2, all reflections)
0.134, 0216
(sinθ/λ)max (Å-1) and completeness (%)
0.5, 24.4
Constraints: 2 rigid bodies
1 isotropic parameter
C9H13NO3
Structure solution: DASH
Refinement program: CRYSTALS
Refinement
Example of good data, lab source
In situ crystallisation study
Water
solvent
Tungsten
gasket
Ruby
chip
Single
crystal
300 µm
Cell setting, space group
Monoclinic, P21/c
a, b, c (Å)
8.9537(11) 5.4541(6) 13.610(4)
β (°)
104.93(2)
Z
4
Multi-scan abs. correction Tmin/Tmax
0.61
No. of measured, independent and
observed [F > 4σ(F)] reflections
3718, 470, 359
Rint
0.08
No. of parameters and restraints
92, 83
R1[F > 4σ(F)], wR2(F2, all reflections)
0.053, 0.103
(sinθ/λ)max (Å-1) and completeness (%)
0.63, 34.4
SIMU, DELU, DFIX [for (N)H
positions] restraints
C6H10N2O2
Structure solution: Sir92
Refinement program: CRYSTALS
Refinement
Example of good data, lab source
Water
solvent
Tungsten
gasket
Ruby
chip
Single
crystal
300 µm
Here would expect
diamond overlaps
Fo
Overlap with
gasket
Shaded reflections
Fc
Increasing data quality – Part I
Synchrotron radiation
Useful properties of synchrotron radiation:
•
•
•
Brilliance  gain in diffracted
intensity compared to a lab source,
i.e. increase in resolution and
completeness
Tuneable wavelength: shortwavelength radiation is accessible
 less absorption and significant
gain in completeness
Small source size: microfocussing is
possible  very small samples can
be investigated; reduction/elimination
of gasket diffraction
S
k′ 2θ
k
1/λ
θ
d
0
nλ = 2d sin θ
Refinement
Example of good data, synchrotron radiation
In situ crystallisation study
300 µm
SIMU, DELU restraints
All H-atoms could be located on difference Fourier maps
Cell setting, space group
Triclinic, P-1
a, b, c (Å)
6.7906(12) 7.3159(4) 15.8428(14)
α, β, γ (°)
86.297(6) 78.924(11) 72.713(6)
Z
2
Multi-scan abs. correction Tmin/Tmax
0.63
No. of measured, independent and
observed [F > 4σ(F)] reflections
6429, 1533, 1294
Rint
0.05
No. of parameters and restraints
172, 100
R1[F > 4σ(F)], wR2(F2, all reflections)
0.045, 0.130
(sinθ/λ)max
(Å-1)
and completeness (%)
0.62, 52
C9H17NO2 . 7(H2O)
Structure solution: Sir92
Refinement program: CRYSTALS
Refinement
Example of good data on a large molecule, synchrotron radiation
Compression study
300 µm
High pressure (1.0 GPa)
Cell setting, space group
Orthorhombic, P212121
a, b, c (Å)
15.9455(4) 21.0511(5) 23.8739(8)
Z
4
Multi-scan abs. correction Tmin/Tmax
0.75
No. of measured, independent and
observed [F > 4σ(F)] reflections
53048, 10032, 7534
Rint
0.05
No. of parameters and restraints
936, 168
R1[F > 4σ(F)], wR2(F2, all reflections)
0.066, 0.216
(sinθ/λ)max (Å-1) and completeness (%)
0.58, 80
SIMU, DELU, DFIX restraints
High pressure (1.0 GPa)
C63H88CoN14O14P . 22 H2O
Structure solution: (SHELXS)
Refinement program: SHELXL
Refinement
Example of good data on a large molecule, synchrotron radiation
Ambient-pressure and temperature study
Ambient pressure
SIMU, DELU, DFIX restraints
Ambient pressure
Cell setting, space group
Orthorhombic, P212121
a, b, c (Å)
15.8260(9) 22.4438(13) 25.4429(16)
Z
4
Multi-scan abs. correction Tmin/Tmax
0.88
No. of measured, independent and
observed [F > 4σ(F)] reflections
101570, 26484, 19937
Rint
0.04
No. of parameters and restraints
917, 168
R1[F > 4σ(F)], wR2(F2, all reflections)
0.073, 0.225
(sinθ/λ)max (Å-1) and completeness (%)
0.72, 96
C63H88CoN14O14P . 23.5 H2O
Structure solution: (SHELXS)
Refinement program: SHELXL
Refinement
Example of good data on a large molecule, synchrotron radiation
Water ordering in channels at high pressure
High pressure (1.0 GPa)
Ambient pressure
Electron density maps generated with shelXle,
Fo-Fc @ 0.31 e-/Å3, Fo @ 0.98 e-/Å3
ShelXle: C. B. Hübschle et al. J. Appl. Cryst. (2011), 44, 1281-1284
Increasing data quality – Part II
Synchrotron radiation
Useful properties of synchrotron radiation:
•
Shorter wavelength  less
absorption, more diffraction data and
smaller diffraction angles
In the lab
•
Ag radiation (0.56087 Å) is now
available as an air-cooled 30 W
microsource (supplier: Incoatec)
 increase in data completeness,
“cleaner” background
S
k′ 2θ
k
1/λ
θ
d
0
nλ = 2d sin θ
Ag radiation in the lab
•
Comparative study on gabapentin
heptahydrate, Incoatec Ag
microsource vs. Mo sealed tube on
a Bruker AXS Apex II diffractometer
Data statistics
Source
Ag-IµS
Mo-ST
Power/ kW
0.03
2.0
Exposure time (s/0.3°)
20
20
<I>
368.8 (64.9)
378.0 (61.0)
<I/σ>
19.6 (3.2)
18.3 (4.7)
Unique data
866 (170)
721 (135)
<Redundancy>
1.5 (0.9)
1.1 (0.7)
<Completeness>/%
40.6 (28.9)
33.7 (22.6)
Rint
0.0306
0.0342
R1 (I<2σ(I))
0.0487 630 refl
0.0532 523 refl.
wR2
0.1025 860 refl.
0.232 705 refl.
Number in parenthesis refer to the highest resolution shell (1.00 – 0.90 Å)
Fore more information: http://www.incoatec.de/?id=101
Ag-IµS, 90 µm beam
300 µm
Mo-sealed tube, 500 µm beam
Further Reading
Further Reading
Acknowledgments
High-Pressure Crystallography
• Prof. Simon Parsons (Edinburgh)
• Dr. Heidrun Sowa (Göttingen)
• Dr. Jürgen Graf (Incoatec)
• Dr. Michael Ruf (Bruker)
Funding
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