chemical crystallography studies on beamline i19 at diamond … · 2019-12-20 · chemical...

Chemical Crystallography studies on

beamline I19 at Diamond Light Source

David R. Allan

([email protected])

Principal Scientist for Beamline I19

Diamond Light Source Ltd

Harwell Science and Innovation Campus

Didcot, Oxfordshire OX11 0DE

United Kingdom

Simon J. Coles

([email protected])

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)



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

&




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

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 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 H9···O14 ρ 0.706 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

doi:10.1021/jacs.8b09364

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

https://doi.org/10.1107/S2052252519006948

chemical crystallography studies on beamline i19 at diamond … · 2019-12-20 · chemical...

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