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Chemical Crystallography studies on
beamline I19 at Diamond Light Source
David R. Allan
Principal Scientist for Beamline I19
Diamond Light Source Ltd
Harwell Science and Innovation Campus
Didcot, Oxfordshire OX11 0DE
United Kingdom
Simon J. Coles
Professor of Structural Chemistry,
Director, UK National Crystallography Service
About NCS
• Supporting UK Chemistry-related academia
– funded to provide access to that which
cannot be accomplished locally
• One of the highest throughput chemical
crystallography labs in the world
• >£5 million centre with State-of-the-Art
instrumentation
• Expert personnel (6 scientists)
• Diamond synchrotron component
• Commercial service
• Outreach and training
• Research areas: quantum crystallography,
structural systematics, structures under
change [Phase Transitions; High Pressure;
Gas Cell], crystal growth and data
management.
About Diamond
• Linear accelerator to 100 MeV from the 90 keV thermionic gun
• Booster synchrotron (158m) to 3 GeV
• Storage ring (3GeV) has a circumference of 562m and is composed
of 24 cells. It operates in top-up mode (10 minute cycles).
Energy 3 GeV
Circumference 561.571 m
Maximum beam current 300 mA
Horizontal emittance 3.14 nm rad
Vertical emittance 8 pm rad
Revolution frequency 533.8 kHz
RF frequency 499.680 MHz
Maximum no. of bunches 936
Time between bunches 2.0 ns – 1.87 µs
Bunch length (rms) 17.1 ps (0.62nC bunch current)
18.0 ps (0.81nC bunch current)
21.2 ps (1.63nC bunch current)
25.6 ps (3.0nC bunch current)
About Diamond
• 8 bending magnet beamlines and 26 beamlines on insertion devices
(3 of these share the same straight section).
• Insertion devices mainly undulators, or permanent magnet wigglers,
but I15 (I15-1) and I12 use superconducting multipole wigglers.
• The beamlines are organised by Science Group: Macromolecular
Crystallography; Soft Condensed Matter; Imaging and Microscopy;
Magnetic Materials; Structures and Surfaces; Crystallography;
Spectroscopy.
• Beamline I19 is in the Crystallography Science Group along with I11
(powder diffraction), I15 (extreme conditions) and I15-1 (xpdf)
Original I19 science programme
(ca 15 years ago)
• Underpinning the frontiers of science and technology
• micron sized crystals
• microporous and mesoporous systems, such as zeolites
• supramolecular assemblies and very large molecules
• catalysis, “smart” materials, optical devices & information storage
• Charge density, from electron density to molecular properties
• understanding materials: e.g. non-linear optic systems, guest-host
materials
• Anomalous dispersion studies – enhanced detail at the edge
• contrast between isoelectronic species & differing oxidation states
• Disorder and its relation to physical properties
• weak scattering features at high Q values
• total-scattering studies
• Structure under change
• catalytic reactions, phase transitions, synthesis/degradation
• environmental cells: pressure, gas exchange, humidity variation
• excited states/ time resolved studies
Beamline design
• Two experiments hutches: high-throughput diffractometer with robotic
sample changer; and large-capacity diffractometer.
Experiments hutch 1 (EH1) - high-throughput diffractometer for
chemical crystallography studies
Experiments hutch 2 (EH2) - heavy-duty diffractometer for complex set
up, bulky sample environment equipment, etc.
Beamline design
• High brightness undulator source
• Simple optics: DCM, horizontal and vertical focusing mirrors, and slits
Linear undulator, 5-25 keV, horizontal polarization
Double-crystal Si [111]
ΔE/E ~ 5 x 10-4 at 7 keV
The horizontal and vertical
focusing mirrors have Si, Rh
and Pt stripes for harmonic
suppression
Focus: 90 µm × 60 µm
Focus: 130 µm × 185 µm
Experiments Hutch 1 (EH1)
High-throughput chemical crystallography studies
3-circle fixed-chi diffractometer. Very
small sphere of confusion & highly
focused beam - extremely small &
weakly scattering crystals
Pilatus 2M detector - rapid data
collections (5 minutes or less)
Robot sample changer enables remote
access users.
Pucks hold 16 crystals
Dewar holds 7 pucks
Total 112 crystals.
Prepare in advance / mail-in capability
Natalie Johnson operating EH1
remotely from Newcastle.
Groups & Remote access
Remote operation requires a fast and stable internet connection and a
workstation with multiple large screens is preferable (essential).
Once connected the beamline staff handover control via the GDA baton.
Beamline operated just as if you
were present in the control room
GDA baton (control) can be passed
between sites: e.g. between users
in a BAG
A BAG is a (logical) grouping of
users with timely, periodic access –
dynamically use time depending on
availability and urgency os service
samples requiring investigation e.g.
NCS – Oxford; Newcastle - Durham
https://doi.org/10.3390/cryst7110336
&
https://doi.org/10.3390/cryst7120360
Additional EH1 sample environments
Oxford Cryosystems Helix open-flow cryostat
- cooling from room-temperature to 30 K.
N.B. Sample mounting must be manual.
HC1 device supplies humidity
controlled air to the sample.
Maximise f’ and f” difference - resolve
position and charge of mixed valence ions
e.g. identify the 5 eV offset between Ga(I)
and Ga(III) by comparing fluorescence
scan for GaCl2 (blue) to Ga13 cluster (red).
Exploiting tunable wavelength
Permanently mounted. X-ray
fluorescence measurements
when tuning the energy to the
edge of a specific element in
the sample.
Karim J. Sutton, Sarah A. Barnett, Kirsten E. Christensen, Harriott Nowell, Amber L.
Thompson, David R. Allan, Richard I. Cooper
Journal of Synchrotron Radiation (2013) https://doi.org/10.1107/S0909049512044007
High resolution X-ray diffraction studies
• X-ray wavelength 0.6889 Å - a balance between Pilatus 2M detector
efficiency and resolution obtained by 2θ positions (up to 2θ of 105 ° or
≈ 0.31 Å)
• Implement screen19 software in initial crystal screening stages to
ensure optimum beam transmission% for each 2θ position.
• Data processing performed using in-house DIALs software followed
by scaling and merging in SORTAV.
• IAM structure solution in WinGX >>> *InvariomTool >>> multipole
refinement in WinXD.
*use database aspherical scattering factors and local site symmetry as
start point for multipole refinement.
O-H···O short strong hydrogen (SSHBs) bonds
Substituted
urea/organic
acids
dO···O < 2.5 Å
O+ –H···O-
Neutron diffraction
determination (VIVALDI-ILL) X-ray diffraction determination combined with
Hirshfeld Atom Refinement
A. O. F. Jones et al., Phys. Chem. Chem. Phys., 2012, 14, 13273-13283. L. K. Saunders et al.,
CrystEngComm, 2019, 21, 5249-5260.
T-dependent proton migration (100 – 400 K)
O+ ···H···O-
O14—H9
H9···O9
O13—H1
H1···O1No T-dependent
migration
A N,N-dimethylurea 2,4-dinitrobenzoic acid 1:1
C N,N-dimethylurea
3,5-dinitrobenzoic acid 2:2
dSSHB 2.4449(6) Å
dSSHB 2.4461(4) Å
B N,N-dimethylurea oxalic acid 2:1
Data collection:
Rmerge 0.0468
99.7% complete to 0.476 Å
Data collection:
Rmerge 0.0485
97.8% complete to 0.413 Å
Data collection:
Rmerge 0.0457
98.9% complete to 0.476 Å L. K. Saunders et al., CrystEngComm, 2019, 21, 5249-5260.
T-dependent migration
dSSHB 2.4415(7) O9…O14
dSSHB 2.4588(8) O1...O13
Refinement up to hexadecapole level; k’ and k’’ fixed at invariom database values; H-
atom model: distances/ADPs from neutron diffraction and scaled using UIJXN (A and
B) or Hirshfield atom refinement (C).
CPSSHB O1—H1 ρ 1.329 eÅ-3
CPSSHB H1···O2 ρ 0.851 eÅ-3
R{F^2} = 0.0323 Rall{F^2} = 0.0370 Rw{F^2} = 0.0574
Fractal dimension plot of
residual density distribution.
Deformation density,
contour level 0.05 eÅ-3
A
δH
+0.245(15)
CPSSHB O1—H1 ρ 1.277 eÅ-3
CPSSHB H1···O2 ρ 0.832 eÅ-3
R{F^2} = 0.0222 Rall{F^2} = 0.0237 Rw{F^2} = 0.0441
contour level 0.05 eÅ-3
B
δH
+0.318(12)
CPSSHB O9—H9 ρ 1.740 eÅ-3
CPSSHB H9···O14 ρ 0.706 eÅ-3
CPSSHB O1—H1 ρ 1.501 eÅ-3
CPSSHB H1···O13 ρ 0.751 eÅ-3
R{F^2} = 0.0270 Rall{F^2} = 0.0292 Rw{F^2} = 0.0574
contour level 0.05 eÅ-3 contour level 0.05 eÅ-3
C
δH
+0.200(12)
δH
+0.200(12)
Charge Density/Quantum Crystallography
• 3 centre, 4 electron bonding in metal complexes; ca 99.5% complete to
0.46Å at wavelength 0.52Å
•A
B
C
D
E
F
Experiments Hutch 2 (EH1)
Experiments requiring bulky sample environment
equipment (in situ crystallography)
Newport diffractometer• -geometry diffractometer - supports
>25 kg at the sample position.
• Can carry a purpose-built closed cycle
cryostat.
• Operated with the GDA software.
• Experiments can be setup without
effecting other (EH1) users.
• Rapid data collections with shutterless
mode Pilatus 300K detector.
High Pressure Crystallography
X-ray beam collimation and sample
viewing has recently been completely
revised.
On-axis sample viewer (OAV).
OAV incorporates a ruby fluorescence
spectrometer for in-situ measurement of
pressure within diamond-anvil cells.
Gas-membrane diamond-anvil cells can
now be used.
The OAV now also allows click-to-centre
sample alignment (same in EH1).
Notable updates
Data processing (CrysAlisPro or Bruker Apex):
- CrysAlisPro: CBF images read-in directly- Apex: images need to be converted to Bruker frame format (script for this).
• Data processing also with in-house Xia2 software.• Much faster than
CrysAlisPro/Apex.• Can be automated for
well behaved systems.
• More rapid feedback during the experiment on the progress of structural change with pressure.
Dynamic masks to account for shading by the diamond-anvil cell
Static masks account for the powder-diffraction lines generated by the tungsten gasket of the diamond-anvil cell
• Zeolitic imidazolate frameworks (ZIFs) promising candidates for use in
separation technologies. Large cavities interconnected by small windows
- can be used as molecular sieves: molecules smaller than the window
size diffuse into the material while larger molecules are rejected.
• Swing effect or gate opening phenomena, resulting in an enlargement of
the windows, have proven to be detrimental to selectivity.
• Isostructural ZIF-8, ZIF-90, and ZIF-65 functional groups of increasing
polarity (−CH3,−CHO, and −NO2) on the imidazole linkers provide control
over the degree of rotation and thus the critical window diameter.
Example study
Vacuum – 10-5 mbar
Flow control up to 130 ml/min
Number of flow cells: 2
Vacuum – 10-5 mbar
Maximum pressure – 150 bar
Number of cells: 8
Flow Cell Capillary Static Cell
N2, Ar, Kr, Ne, CO2, CO, SO2, NO, N2O, CH4, O2, H2
Current Gases
Gas Cell Equipment
44
Gas Cell Rig
Pneumatic valve Pressure Relief Valves
Alicat MFCPressure TransducersGas Inlets
Lines to gas cell
44
Gas Cell Rig Control
Open/Close
Pneumatic valves
To gases (1-3)
Monitor
Pressure
Plot
Pressure
Control the
mass flow of a
selected gas
0 to 200
ml/min
Exhaust Rig (5)Open sample
lines (4)
Vacuum 10 bar CO2
Solvated Vacuum 10 bar CO2
128
20
16 1519
190 187
0
20
40
60
80
100
120
140
160
180
200
220
240
Ele
ctr
on
in
po
re (
pla
ton
sq
ue
eze
)
gs_
102
_r1
-4
gs_
10
0
gs_
10
1
gs_
10
2_
r5-8
gs_
10
3
gs_
10
4
gs_
10
5
44
Case Study – MOF gas sorption
Co(bpy)1.5(NO3)2
1 32 4 65 7
Solid-State Molecular Organometallics (SMOM)
• Impossible complexes and catalysis: Solid/gas Single–Crystal to
Single–Crystal (SC–SC) hydrogenation
M
P
P
R R
RR
Ln
Molecular Organometallic Anion Oh–microenvironment
Solid–state Molecular
OrganoMetallic Chemistry and
Catalysis
(C)
(A)
SMOM
(B)
HRhP
P HH
H
+ H2
SC–SC Cy2
Cy2
[1–NBA][BArF4]
[1–NBD][BArF4]
[BArF4]
β
SC–SC = single–crystal to single–crystal
298 Kn
Variation of chelating ligands leads to changes in structure & reactivity
JACS, 2018, DOI:10.1021/jacs.8b09364
Variation in s–complex structure & bondingChanging the phosphine & hydrocarbon
h2h2 s–alkane h1 s–alkaneagostic &
encapsulated alkane
Solid–State Molecular Organometallic Chemistry (SMOM–Chem) using {RhL2}+
Periodic DFT, QTAIM, NBO
Time Resolved Photocrystallography -
Steady-State Data Collection
- Lifetimes longer than the diffraction experiment
- Can be used to study irreversible reactions, cryotrapped
intermediates or systems which are in light induced equilibrium.
Time
X-r
ays
Timeirra
dia
tion
exci
tati
on
Time
System excitation
Light
Full x-ray data setFull x-ray data set
Ground state Photo induced state
X-ray Chopper
X-r
ays
time
Laser pulse(5 ns width)
X-ray pulse(1 ms width)
Time-delay
- 1 ms X-ray pulse generated by
mechanical chopper
- Synchronized with the pulse train
from 10 Hz laser
- Electronic delay between the laser
and X-ray can be selected by the
user
X-ray Pulse
X-ray Chopper Chopper
Chopper
X-ray Chopper
Pump-probe data collection
- Need a reversible reaction which can be
activated (pumped) at a given time.
- Pumping synchronised to the pulsed X-rays
[or detector]
- After the system has been pumped, if the
system is probed at the same time-delay
after activation, the system will appear static
or suspended in time!
- Therefore an entire dataset can be obtained
in the normal manner.
X-r
ays
irra
dia
tio
nex
cita
tio
n
Pump-probe data
collection
Time-delay
Pilatus Gating (instead of chopper)
- Pilatus 300K, has a readout time of 2.3 ms
- Pilatus can be gated to 200 ns (acquire / not acquire)
- Can use the gating of the pilatus to “pulse” the X-ray beam
X-r
ays
irra
dia
tion
exci
tati
on
Pump-probe data collection
Time-delay
Pilatus Gating (instead of chopper)
X-r
ays
irra
dia
tion
exci
tati
on
Pump-multi-probe data collection
1 2 3 4 5 106 7 8 9 1 1 1 1 1 1 1
Entire time-resolved time series in one data collection (2 hours)
Better comparison between delay-times (same crystal, temperature,
radiation damage and laser excitation).
Pump-multi-probe
Example
O-bound
nitrito
N-bound
nitro
- These compounds have tuneable lifetime depending on
temperature
- New atom position upon excitation
- Good test systems for time-resolved setups
Beware – Radiation Damage is rife…
https://doi.org/10.1107/S2052252519006948