exploring polymorphism in molecular compounds using high ... · • molecular organic materials,...

High-Pressure Crystallography

Francesca P. A. Fabbiani Emmy-Noether Jr. Research Group

• Introduction to high-pressure research

• Experimental setup

• Collecting high-pressure data, solving and refining structures

• Molecular organic materials, single crystals

Welcome

Part 1

Part 2 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

Dr. Michael Ruf Product Manager, SC-XRD Madison, WI, USA

Introduction to High-Pressure Research

• 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)

• Chemistry/molecular compounds (e.g. amino acids, molecular magnets, pharmaceuticals)

• Proteins, pressure-induced denaturation, folding

High-Pressure Research

Mao H , Hemley R J PNAS 2007;104:9114-9115 ©2007 by National Academy of Sciences

Range of pressures and temperatures now accessible with static compression techniques in the laboratory.

Source: Martin Chaplin, http://www.lsbu.ac.uk/water/phase.html

Phase diagram of water

• Industrial applications, e.g. pressure treatment of food

• Origin of life/ sustained life at the bottom of the oceans

• Access new materials, probe intermolecular interactions

• Understand polymorphic transformations

• Interplay with theory

High-Pressure Research

Source: Wikimedia Commons


Cubic BN

Beta sheet

Paracetamol


(1000 atmospheres ≈ 1 kbar = 100 MPa = 0.1 GPa)

GPa

Non-equilibrium pressure of H2

gas in intergalactic

space

104 103 10 10-1 10-2 10-16 10-36 108 1 Earth

atmosphere at altitude of 300

miles

Sea level

Centre of the Sun

Centre of the Earth

Centre of Jupiter

Pressure inside a light

bulb

Ice skater standing

on ice

Peak pressure of fist on concrete

during karate strike

Greatest depth in oceans

Graphite becomes diamond

Hydrogen becomes metallic

10-5 10-4 102

Molecular materials

High-Pressure Scale

Orders of magnitude available for pressure variation >> temperature variation

Experimental Setup

1958

Pressure Generation for in situ XRD: Diamond-Anvil Cell

First diamond anvil cell at NIST Gaithersburg Museum

Source: G. J. Piermarini, Wikimedia Commons

DAC manufactured by Dr. H. Ahsbahs

F. P. A. Fabbiani et al. CrystEngComm (2010), 12, 2354-2360

5 cm

2009 Aluminium DAC mounted on a goniometer head

P= F/A (kgms-2/m2 = N/m-2 = Pa)

Choose your DAC carefully: backing plates material, diamond cut, purity and culet size, gasket hole size, DAC opening angle

Pressure Generation for in situ XRD: Diamond-Anvil Cell

Tightening screws

Backing plate

Diamond Diamond

Gasket

F

F

A

Diamond

Ruby

Sample

• 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

• 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

Equipment for DAC preparation

DAC Loading

Three main sample loading methods available

Sample loading methods depend on:

• Nature of the sample under investigation

• Aim of experimental investigation

“Fathers” of high-pressure research: G. H. J. A. Tammann (1861-1938), P. W. Bridgman (1882-1961)

DAC Loading

300 µm 300 µm

The focus here is on molecular organic materials for single-crystal X-ray diffraction

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

DAC Loading

p

T

S L

V

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

DAC Loading

Approach 2: In situ crystallisation and growing from the melt

heat

cool

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

DAC Loading

• Introduction to high-pressure research

• Experimental setup

• Collecting high-pressure data, solving and refining structures

Outline

Part 1

Part 2

Molecular organic materials, single crystals

Collecting high-pressure data, solving and refining

structures

• 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)

Data collection in transmission mode

Data Collection

~ 144 mm Short collimator and long beamstop

Set up @ GZG Göttingen

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

2θ

Incident beam I

Diffracted beam D ΨD

Collimator Axis of symmetry

Data Collection

Steel support of the DAC starting to obscure the detector

ω

For one orientation of the DAC, the accessible region of reciprocal space is determined by the detector distance and the DAC opening angle

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)

R. J. Angel et al. Phase Transitions (1992), 39, 13-32

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

Set up @ GZG Göttingen

Data Collection

structure solution

data collection

data processing

structure refinement

Absorption and shadowing

Limited sampling of reciprocal space data completeness and resolution

Sample scattering power (and size)

Background

X-ray Crystallography

2θ

Incident beam I

Diffracted beam D ΨD

Collimator Axis of symmetry

Coverage of reciprocal space

Data Completeness

• 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

Increasing Data Completeness

Rotate by 120° and collect

Rotate by 120° and collect Collect

On a 3-circle diffractometer

• Data indexing identify reflections arising from sample

Data Processing

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)

Harvesting reflections


Data Processing

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

Reciprocal lattice viewer


• Data integration mask out regions of detector obscured by the DAC; choose appropriate resolution; background correction

Data Processing

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

Twins can be easily handled

Try to keep the box size small. If problems with convergence: uncheck this option

If background is jumpy choose high frequency; otherwise reduce



Data Processing

Threshold for strong reflections: lower this to, e.g. 8 for weak data

This option might be useful for synchrotron data

For using dynamic masks generated with an external program

Typical frames from CCD Area Detector

Dynamic masks: A. Dawson et al. J. Appl. Cryst. (2004), 37, 410–416; N. Casati et al. J. Appl. Cryst. (2004), 40, 620-630

Powder ring from Beryllium

backing discs (now almost

obsolete)

Powder ring from steel gasket

almost invisible at 2θ = 0 (gasket and

beam size dependent)

Shading from DAC opening

angle

Diamond reflection

Dynamic mask for integration

Sample reflection

Data Processing



Data Processing

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

• 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



• Data merging crucial step; robust-resistant and experimental (1/σ2) weighting scheme with SORTAV

• Structure solution direct methods, global optimisation methods (borrowed from powder diffraction), molecular replacement, etc.: numerous programs available!

Data Processing

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

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

Refinement program: CRYSTALS

C9H13NO3 Structure solution: DASH

Refinement

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



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

300 µm

Single crystal

Tungsten gasket

Water solvent

Ruby chip

SIMU, DELU, DFIX [for (N)H positions] restraints

C6H10N2O2

Refinement program: CRYSTALS Structure solution: Sir92

Refinement

Example of good data, lab source In situ crystallisation study

Fo

Fc

Shaded reflections

Here would expect diamond overlaps

Overlap with gasket

300 µm

Single crystal

Tungsten gasket

Water solvent

Ruby chip

Refinement

Example of good data, lab source

Increasing data quality – Part I

• Brilliance gain in diffracted intensity compared to a lab source, i.e. increase in resolution and completeness

• Tuneable wavelength: short-wavelength 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

k

k′

d

2θ

θ 0

S

1/λ

θλ sin2dn =

Synchrotron radiation Useful properties of synchrotron radiation:

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



Rint 0.05



(sinθ/λ)max (Å-1) and completeness (%) 0.62, 52

300 µm

C9H17NO2 . 7(H2O)

SIMU, DELU restraints

Refinement program: CRYSTALS Structure solution: Sir92

Refinement

All H-atoms could be located on difference Fourier maps

Example of good data, synchrotron radiation In situ crystallisation study

Cell setting, space group Orthorhombic, P212121

a, b, c (Å) 15.9455(4) 21.0511(5) 23.8739(8)

Z 4



Rint 0.05




300 µm

C63H88CoN14O14P . 22 H2O

SIMU, DELU, DFIX restraints

Refinement program: SHELXL Structure solution: (SHELXS)

High pressure (1.0 GPa)

Refinement

High pressure (1.0 GPa)

Example of good data on a large molecule, synchrotron radiation Compression study

Cell setting, space group Orthorhombic, P212121

a, b, c (Å) 15.8260(9) 22.4438(13) 25.4429(16)

Z 4



Rint 0.04




SIMU, DELU, DFIX restraints

Refinement program: SHELXL Structure solution: (SHELXS)

Ambient pressure

C63H88CoN14O14P . 23.5 H2O

Refinement

Ambient pressure

Example of good data on a large molecule, synchrotron radiation Ambient-pressure and temperature study

Water ordering in channels at high pressure

Electron density maps generated with shelXle, Fo-Fc @ 0.31 e-/Å3, Fo @ 0.98 e-/Å3

Ambient pressure High pressure (1.0 GPa)

Refinement

Example of good data on a large molecule, synchrotron radiation

ShelXle: C. B. Hübschle et al. J. Appl. Cryst. (2011), 44, 1281-1284

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

k

k′

d

2θ

θ 0

S

1/λ

θλ sin2dn =

• Shorter wavelength less absorption, more diffraction data and smaller diffraction angles

Increasing data quality – Part II

Synchrotron radiation Useful properties of synchrotron radiation:

Ag radiation in the lab

• Comparative study on gabapentin heptahydrate, Incoatec Ag microsource vs. Mo sealed tube on a Bruker AXS Apex II diffractometer

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)

Data statistics

Ag-IµS, 90 µm beam Mo-sealed tube, 500 µm beam

Fore more information: http://www.incoatec.de/?id=101

300 µm

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