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POWDER X-RAY DIFFRACTION STUDY OF ZEOLITIC IMIDAZOLATE FRAMEWORK-8
Owen J. Gledhill
ID22, European Synchrotron Radiation Facility – ESRF,
Grenoble, France
ABSTRACT
Powder X-ray diffraction was used at ID22 at the ESRF to study the zeolitic imidazolate
framework ZIF-8. ZIF-8 was synthesised using a variety of methods, all of which were
adapted from previously reported studies. The diffraction patterns of the samples from the
different syntheses were analysed using Pawley and Rietveld refinement techniques.
Samples produced in DMF, ethanol and acetone produced ZIF-8 in good agreement with
the literature. It was decided that the samples produced in DMF were most suitable for gas
adsorption measurements. The effects of loading CO2 onto the samples up to pressures of
12.5 bar were studied. The gas adsorption measurements showed an expansion of the unit
cell as CO2 pressure was increased. It was seen that CO2 occupied the pores of the
framework but with no specific interactions between the framework and the gas molecules.
Theoretical calculations on the gas position, average gas loading and pore structure were
performed for comparison with the empirical findings. In general, there was good
agreement between the two but it would be useful to perform further measurements with
different gases as well as industrially relevant gas mixtures. There was an issue with
solvent remaining in the pores once synthesised, even after evacuation of the samples.
Further studies would include solvent exchanges in an effort to completely remove it and
thus make gas adsorption measurements more accurate.
LAY REPORT
Zeolitic Imidazolate Frameworks (ZIFs) such as ZIF-8 are a class of compounds which
have recently garnered much interest due to the properties that they possess. Specifically,
they tend to be highly crystalline, highly porous and ZIF-8 in particular is extremely
thermally and chemically stable [10]. These properties make ZIFs particularly attractive as
candidates for applications such as gas storage, gas separation and catalysis.
This project aimed to investigate the synthesis of ZIF-8 using a range of synthetic
techniques based on those reported in previous studies, followed by analysis of the samples
to choose the most appropriate candidate for gas adsorption measurements. Also to
examine the effect of adsorbing CO2 gas onto the ZIF-8 samples and gain an insight into
the behaviour of the gas once inside the pores.
The European Synchrotron Radiation Facility’s high resolution powder X-ray
diffraction (PXRD) beamline, ID22, was used to collect diffraction patterns. Patterns were
collected on all the as synthesised samples as well as selected samples which had CO2 gas
loaded onto them over a range of pressures. The diffraction patterns were indexed and
refined to gain structural information as well as being the basis for calculating the position
of gas molecules within the pores. Several pieces of specialised software were used to
perform these calculations such as TOPAS which was used for refinements; Materials
Studio which was used for 3D modelling of the structures and gas position determination;
and Mercury which was used to model the pore structures.
It was seen that ZIF-8 was successfully synthesised using several of the methods
tried and that they were in accordance with the literature data. However, for the samples
produced in DMF, there was an issue with solvent remaining in the pore and a ZnO
impurity being present. The gas adsorption experiments showed that CO2 was readily
adsorbed into the pores of ZIF-8 which was indicated by an increasing lattice parameter as
the gas pressure was increased. It was shown that there were no specific interactions
between the framework and the CO2 molecules which was probably due to the fact that all
the metal binding sites are occupied in ZIF-8. The theoretical calculations showed good
agreement with the empirical results.
There are some limitations with the results of the study. For example, the fact that
there was an impurity in some of the samples and solvent remained in some of the pores,
could reduce the accuracy of the gas adsorption results. This is because the pores would
already be partially filled, and hence prevent the maximum amount of CO2 being adsorbed.
Also, another issue faced was that ZIF-8 appeared to be very sensitive to radiation and only
very short scans could be taken. This suggests that PXRD isn’t a perfect technique for the
analysis of ZIF-8 and it would perhaps benefit from being coupled with other techniques
such as elemental analysis and spectroscopy.
COMPANY OVERVIEW
The European Synchrotron Radiation Facility (ESRF) is Europe’s most powerful
synchrotron located in Grenoble, France and is an internationally renowned research
institute. More than 6000 users and around 600 staff perform experiments in an
increasingly wide range of scientific areas every year at one of the ESRF’s 41 highly
specialised beamlines. From the 1500 experiments performed yearly at the ESRF, over
2000 publications are produced which equates to over 20,000 since its inception in 1994
[1].
Funding
The ESRF operates with a budget of around 80M € a year which is provided by the ESRF
member states as well as some additional contributors [2].
ESRF Member contributions:
27.5% France
24% Germany
13.2% Italy
10.5% United Kingdom
6% Russia
4% Spain
4% Switzerland
5.8% Benesync (Belgium, The Netherlands)
5% Nordsync (Denmark, Finland, Norway, Sweden)
Additional contributors:
1.5% Israel
1.3% Austria
1% Poland
1% Portugal
1.05% Centralsync (Czech Republic, Hungary, Slovakia)
0.3% South Africa
ESRF history: [2]
1975: Idea for a European third-generation synchrotron source
1988: Signing of the agreement between the governments of 12 Member States
1992: First electron beam in the storage ring. Commissioning phase.
1994: User operation begins with 15 beamlines
1998: Forty beamlines in operation
2009: Start of the ESRF Upgrade Programme
2011: Inauguration of the first Upgrade Beamline
2015: Completion of Phase I Upgrade Programme
The ESRF and similar facilities
The ESRF is Europe’s premier synchrotron facility, which operates at 6 GeV. However,
there are many other synchrotron facilities in Europe, such as Diamond in the UK (3 GeV)
and ALBA in Spain (3 GeV); as well higher energy synchrotrons outside Europe like
SPring-8 in Japan (8 GeV) and the APS in the USA (7 GeV) [3].
The ESRF differs from these other facilities as it employs staff from more than 40
countries who are typically on short term contracts which promotes innovation and ensures
that new ideas are always being brought to the ESRF [1].
Beamlines and science at the ESRF
Figure 1 shows the layout of the ESRF with the beamlines running tangential to the storage
ring as well as where the different types of beamlines are positioned.
Figure 1. Layout of ESRF beamlines after completion of Phase I upgrade [1].
There are two types of beamline based on the way in which X-rays are produced.
These being insertion device (ID) or bending magnet (BM) beamlines. Most BM
beamlines are CRG (collaborating research groups) beamlines and are not operated by the
ESRF but by external institutions from ESRF member states [1].
The diverse range of techniques used at the beamlines is what allows such a wide
range of science to be carried out at the ESRF. The ESRF currently performs research in
areas from chemistry to paleontology, and physics to biochemistry as shown in figure 2.
Figure 2. Scientific research areas studied at the ESRF [4]
Users
Users at the ESRF help to drive this diversification of science carried out at the ESRF.
Users from external institutes submit proposals for time at one of the beamlines to perform
their experiments. Proposals are considered twice a year and are reviewed by independent
review committees [1]. They are chosen using criteria such as scientific merit, and
beamtime is also allocated according to the percentage stake each member state has in the
ESRF. Beamtime is free for users of member countries if their research is made public [5].
However, the number of industrial users is increasing at the ESRF as they have access to
techniques that are not available at any other facilities. Figure 3 shows some of the
industrial sectors that use the ESRF.
Figure 3. Industrial sectors using the ESRF [4]
My Role at the ESRF
I am part of the experiments division which is one of six divisions at the ESRF which
covers all aspects of the organisation. The experiments division is further divided into
beamline groups which have similar research areas. I work on beamline ID22 which is one
of five in the structure of materials group as shown in figure 4.
Figure 4. Organisation of structure of materials group [6]
Stru
ctu
re o
f M
ater
ials
Gro
up
ID01: Microdiffraction imaging
ID03: Surface diffraction
ID11: Materials science, time resolved diffraction
ID15A/B: High energy diffraction/scattering
ID22: Powder diffraction Me
ID22 is the ESRF’s high resolution powder diffraction beamline and it is suitable for a
number of diffraction measurements; a few of which are listed below [7]:
Structural studies: Solving and refinement of crystal structures
Dynamic and in-situ studies: Observation of change of structure as a function of
time, temperature, voltage etc…
High throughput studies: Sample changing robot allows up to 75 samples to be
measured in succession.
As a trainee at ID22, my main role is to gain an understanding of powder X-ray diffraction
(PXRD) and crystallography at a synchrotron facility. This is achieved by completing a
project on the study of metal organic frameworks. The project involves the synthesis of
samples whose structures are studied with PXRD as well as gas adsorption experiments
that are studied by the same technique. Another focus of project at ID22 is the analysis of
data collected on the beamline using several complex software packages.
As well as this, my work has allowed me to begin to understand the working and
running of a synchrotron and see some of the vast range of science that is studied at the
ESRF.
SCIENTIFIC REPORT
1. Introduction
1.1 MOFs and ZIFs
The term metal organic framework or MOF was first coined by Yaghi and his group in
1995 [8]. MOFs (sometimes also referred to as porous coordination polymers or porous
coordination networks) are a class of compound that as the name suggests, are made up of
an inorganic and an organic section. Typically these are a metal ion or cluster and organic
ligands which are bound primarily with coordination bonds [9] to produce porous lattices.
The strength of the coordination bonds within MOFs is sufficient to produce well defined
framework structures that are strong enough to be permanently and highly porous. They
also tend to be very crystalline materials. This high degree of crystallinity allows
characterisation by various diffraction methods [9]. Theoretically there are endless
combinations of metal ions and linker molecules that could make MOFs which helps to
explain their tuneability. As such, they have potential applications in areas such as
catalysis and gas separation which has seen them become a widely studied class of
compounds in the last decade.
In recent years, a large number of MOFs have been synthesised using imidazolate
organic linker molecules [10][11][12][13]. This sub class of MOFs is known as zeolitic
imidazolate frameworks (ZIFs). They are formed from Zn or Co cations along with
imidazole linkers (Im) [14]. One of the reasons ZIFs have gained such considerable
attention of late is due to their structures having striking similarities with naturally
occurring zeolites. For example, the M-Im-M angle (where M = Zn or Co) is close to 145 o
which is very similar to the Si-O-Si angle in many zeolites as seen in figure 1 [10].
Figure 1. Similar bridging angles in ZIFs (left) and Zeolites (right) [10]
Following this observation, it was predicted that new ZIFs can be synthesised based
on the structure of already characterised zeolites. As a result, over 90 ZIF structures have
been reported in recent years [15]. ZIFs possess advantageous characteristics of both
MOFs and zeolites such as high crystallinity found in zeolites; high thermal and chemical
stability; and the ability to be easily functionalised like MOFs [10][14]. One of the most
widely studied ZIFs is ZIF-8[10][11][16][13].
ZIF-8 is formed from tetrahedrally coordinated Zn2+ ions and 2-methylimidazole
linkers (mIm); taking the form Zn(mIm)2. It has large, ~11.6 Å diameter pores connected
by narrow hexagonal channels with a diameter of ~3.4 Å seen in figure 2 [10][17]. It is
these distances that mean ZIF-8 has potential applications in gas storage and separation of
industrial relevant gas mixtures [9] as well as catalysis [18].
Figure 2. ZIF-8 structure showing hexagonal pore opening [17](supporting info)
1.2 Miller Planes and Bragg’s Law [19]
Crystalline materials, by definition, have long range order throughout their structure. This
can be represented by sets of parallel planes between lattice points known as Miller Planes.
Each set of planes is represented by the inverse intercepts of the unit cell parameters (h, k,
l). The way monochromatic X-rays interact with these planes is the basis for Bragg’s law.
It provides the condition for an X-ray to be diffracted by a particular set of Miller planes. If
two monochromatic X-rays of the same wavelength (λ) hit two parallel planes spaced at
distance, d, the beam hitting the lower plane will have to travel the distance AB+BC
further as shown in figure 3. The angle of incidence and angle of diffraction is represented
by θ.
Figure 3. X-rays hitting miller planes in a crystal lattice to show difference in path length.
From figure 3, it can be seen that:
𝐴𝐵 + 𝐵𝐶 = 2𝑑𝑠𝑖𝑛𝜃 (1)
The reflected X-rays are in phase and constructively interfere with one another when the
path length difference is an integer number of wavelengths:
𝐴𝐵 + 𝐵𝐶 = 𝑛𝜆 (2)
Combining equations 1 and 2 gives us Braggs Law:
2𝑑𝑠𝑖𝑛𝜃 = 𝑛𝜆 (3)
When Bragg’s Law is satisfied, a peak in a diffraction pattern is observed.
1.3 Powder X-ray diffraction
Powder X-ray diffraction (PXRD) is an analytical technique that is typically used to
characterise crystalline materials. PXRD uses a powdered (polycrystalline) sample where
ideally all orientations of the crystal are equally represented in the diffraction pattern.
At the ESRF, the synchrotron provides X-ray radiation which is fired at a powdered
sample where it diffracts. Each crystal in the sample diffracts to give a spot. As all of the
orientations of the crystal should be present in the powder sample, the spots develop into a
series of concentric circles known as Debeye Scherrer rings. The diffracted X-rays are
recorded by a detector and converted to a diffraction pattern which is usually plotted as
Intensity vs. 2θ.
A
B
C
θ
θ
d
θ
θ
Figure 4. Schematic representation of PXRD
The diffraction pattern can then be used to deduce structural information such as lattice
parameters and space group.
1.3.1 Refinements
During the placement, diffraction patterns have been refined using two methods: Pawley
and Rietveld refinement.
Firstly, Pawley refinement tries to fit the peaks in the empirically derived
diffraction pattern using the supposed unit cell parameters and symmetry suggested by
DASH or the literature. Except for the lattice points, Pawley refinement assumes no
structural information such as the size or position of atoms within the unit cell and only
considers lattice points. As such, Pawley refinement is a technique used to confirm
whether the indexing is correct and whether the sample has multiple phases or impurities in
it.
Secondly, Rietveld refinement utilises structural information about the sample. This
data is typically reported in the form of a .cif file. It contains atom coordinates from a
theoretical or previously reported model which allows TOPAS to refine the empirical
diffraction pattern by trying to minimise the difference between the two. A Z-matrix is
used to minimise the number of parameters and to stabilise the refinement. Z-matrices can
be used to define a rigid body, e.g. the linker molecule, which is a part of the framework.
The Z-matrix defines certain atoms in fixed positions with respect to others. For ZIF-8, the
mIm ring is defined by a Z-matrix. There are also other user defined parameters that reduce
the difference between the two models such as occupation of sites and bond lengths.
In addition to the structural information, the TOPAS input (.inp) files for both
Pawley and Rietveld refinements also contain variables that define peak shape, refine the
zero point error and the background; amongst others.
1.3.2 R Factor [24]
The reliability factor; or R factor; is a useful quantitative factor that allows the
experimental and theoretical data in a Pawley or Rietveld refinement to be compared.
TOPAS provided an Rexp and an Rwp factor. Rwp (R weighted profile) can be used as a
measure of quality of fit between the theoretical and experimental diffraction patterns
during a refinement. It is displayed as a percentage figure and represents the difference
between both models. Rexp (R expected) describes the statistically best fit between the two
models and ideally, the Rwp value should be as close to this as possible. In both cases, the
lower the percentage, the better.
2θ
Synchrotron radiation (X-
rays) Powder Sample
Detector
I 2θ
1.4 ESRF – The Synchrotron [20]
The X-rays used for diffraction are produced by the synchrotron. The synchrotron is a
particle accelerator comprised of three major components. The linear accelerator (Linac),
which produces the electrons; the booster synchrotron, which accelerates the electrons to
relativistic speeds and their final energy of 6 GeV; and finally, they are injected into the
storage ring where this energy is maintained.
Figure 5. ESRF layout [20]
The ring consists of a series of bending magnets and insertion devices that produce
X-rays. The primary purpose of bending magnets is to maintain the circular orbit of the
electrons but as the direction of electrons is changed, synchrotron radiation is released (as
shown in figure 6) tangentially to the plane of the electron beam. The radiation released
covers a wide range of the electromagnetic spectrum from microwaves to X-rays and is
much less brilliant than the X-rays emitted from insertion devices.
Figure 6. Bending magnet [20]
Insertion devices are a series of magnets with alternating polarity that cause the
electrons from the storage ring to follow a wavy trajectory. At each bend, the radiation
emitted constructively interferes with that from the other bends to produce a very focused,
brilliant beam of X-rays. Brilliance is a measure of the number of photons that can be
concentrated on a specific spot within a given time.
Figure 7. Insertion device or undulator [20]
1.5 ID22
ID22 is located at an insertion device and can work with X-rays in the energy range 6-
80 keV [21]. ID22 uses a channel cut Si(111) monochromator which allows a single
wavelength to be selected from the undulator spectrum. There is no focusing of the X-ray
beam as a relatively large area of sample needs to be illuminated to ensure a good powder
average is collected [22]. The diffractometer at ID22 is comprised of a bank of nine
detectors that scan vertically to measure emission intensity as a function of 2θ. For
crystallographic studies, powdered samples in glass capillaries are typically spun to ensure
all crystal orientations are represented equally [22].
1.6 ZIF-8 structure
As mentioned in section 1.1, ZIF-8 is formed from Zn2+ ions that are tetrahedrally
coordinated to 2-methylimidazole (mIm) rings and it takes the form Zn(mIm)2. The mIm
rings are bridged between two zinc atoms. As such, the Zn atoms in ZIF-8 have no
available metal binding sites. Also, as the mIm ring essentially acts as a ligand with -1
charge, the electron density within the ring is delocalised somewhat like a
cyclopentadienyl ligand.
Typical bond distances between the Zn atoms and the nitrogen atoms on the mIm
rings are 2.096Å. This creates a framework that has hexagonal pores linked by six Zn
atoms as well as smaller square channels where the corners are four Zn atoms. It has been
reported in the literature that the hexagonal pore opening is ~3.4Å [10].
1.7 Aims
To research ZIFs and MOFs
To synthesise ZIF-8 using a range of methods
Characterise synthesised samples using PXRD as the primary characterisation
technique
Perform gas adsorption experiments on samples of ZIF-8
Use computer modelling to construct 3D representations of ZIF-8 as well as theoretical
gas adsorption calculations.
2. Experimental
2.1 Synthesis
The naming of samples have been chosen based on an arbitrary system by the order in
which they were synthesised and to be easily distinguished from one another. They are
described in the following section but will be referred to by their name for the remainder of
the report.
2.1.1 DMF (solvothermal):
These syntheses were adapted from the procedure reported by Yaghi et al. [10]. A typical
synthesis sees 7 mmol Zn(NO3)2•6H2O and 5.85 mmol 2-methylimidazole (mIm) dissolved
in 25 ml DMF (dimethylformamide) in a 50 ml glass beaker. The reaction mixture was
then transferred to a sealed 30 ml PTFE container. The mixture was then heated from room
temperature (~22oC) at 5oCmin-1 until a temperature of 140oC was reached; at which point,
the temperature was held constant for 24 hours. The reaction mixture was then cooled at
0.5oCmin-1 back to room temperature. The washing and drying procedures differ slightly
for the different samples:
OG1 and OG4: Washed with 3×3 ml portions of DMF followed by drying at 60oC for 3
hours.
OG6: Washed with 5×3 ml portions of DMF portions then dried at 75oC for 4 hours.
Followed by washing in 50 ml of 1M NaOH and rinsing with deionised water. Dried for
a further 4 hours at 75oC.
OG9: Washed twice with 40ml portions of 1M NaOH and rinsed thoroughly with water
before drying at 75oC for 4 hours.
OG10-1, and OG10-3: Washed with 5×3 ml portions of DMF then dried at 75oC for 7
hours.
OG10-2: Washed with 5×3 ml portions of DMF then dried at 75oC for 7 hours.
Evacuated for 7 hours at 75oC followed by 48 hours at room temperature.
2.1.2 Ethanol/Acetone (solvothermal):
These syntheses were based on procedures previously reported by Cravillon et al. [16].
The same method was followed for each of these syntheses but using either ethanol or
acetone as the solvent. A typical synthesis used Zn(NO3)2•6H2O, mIm and solvent in the
ratio 1:8:700. The Zn(NO3)2•6H2O and mIm were both dissolved in equal amounts of
solvent and the Zn solution was then added slowly to the mIm solution. The reaction
mixture was stirred for 2 hours at room temperature. The resulting precipitates were
collected by centrifugation and re-suspended in methanol. This mixture was centrifuged a
second time and the precipitate was dried at 70oC for 5 hours.
OG7: Ethanol synthesis
OG8: Acetone synthesis
2.1.3 Aqueous (hydrothermal):
These syntheses were based on procedures previously reported by Kija et al. [13].
Typically, 2.5 mmol of Zn(NO3)2•6H2O was dissolved in 6 ml of deionised water and
25 mmol of mIm was dissolved in 16 ml of deionised water. The Zn solution was then
slowly added to the mIm solution. At this stage, the method differs slightly for different
samples:
OG2: Reaction mixture was transferred to a 50 ml PTFE beaker and sealed shut. The
mixture was then heated from room temperature (~22oC) at 5oCmin-1 until a temperature
of 140oC was reached; at which point, the temperature was held constant for 24 hours.
The reaction mixture was then cooled at 0.5oCmin-1 back to room temperature.
OG5: Reaction mixture was left at room temperature for 48 hours.
Both samples were subsequently washed with 30 ml deionised water and the product was
collected by filtration. Table 1. Yields from different synthetic techniques assuming solid product is ZIF-8
Sample name Solvent Yield (limiting reagent)
OG1 DMF 24% (mIm)
OG2 Water 43% (Zn)
OG4 DMF 24% (mIm)
OG5 Water 58% (Zn)
OG6 DMF 18% (mIm)
OG7 Ethanol 15% (Zn)
OG8 Acetone 40% (Zn)
OG9 DMF 35% (mIm)
OG10-1 DMF 30% (mIm)
OG10-2 DMF 32% (mIm)
OG10-3 DMF 31% (mIm)
All solvents and reagents were purchased from Sigma-Aldrich and used as supplied.
2.2 PXRD measurements:
Samples were loaded into 1 mm diameter borosilicate glass capillaries for most
measurements except gas adsorption measurements which used 1 mm quartz glass
capillaries. More information on preparing samples can be found in section A4 of the
appendix.
2.2.1 Radiation damage measurements:
To determine the lifetime of a sample in the X-ray beam, several scans were run on each
sample at the same position of the capillary. Typically, four scans were run at two minutes
each per sample in the same position. All measurements were taken at room temperature.
2.2.2 Measurements for refinements:
The table below details the information about the scans performed on each sample,
including wavelength, number of scans and 2θ range of the scans. The distance translated
between positions refers to the distance that the capillary is moved to ensure that a new
section of powder is hit by the X-ray beam and minimise the effect of radiation damage.
All measurements were taken at room temperature.
Table 2. Information on scans taken over different samples
Sample
name
Wavelength
/ Å
No. of
scans
2θ range / o
Length
of scan
/ min
No. of
scans at
each
position
Distance
translated
between
positions /
mm
OG1 0.496007 14 1 to 16 1 1 1.2
OG2 0.400737 1 -5 to 25 2 1 n/a
OG4 0.400737 3 -5 to 25 5 1 1.3
OG5
(capillary 1)
0.399740 24 -5 to 25 1.5 1 1.3
OG5
(capillary 2)
0.399740 28 -5 to 25 1.5 1 1.3
OG6 0.399830 26 0 to 20 2 2 1.3
OG7 0.354205 9 -4 to 20 4 1 1.4
OG8 0.345205 4 -4 to 20 4 1 1.4
OG9 0.345205 20 0 to 20 2 1 1.3
OG10-1 0.345335 1 -5 to 25 6 1 n/a
OG10-2 0.345335 1 -5 to 25 6 1 n/a
Some of the samples start measuring at negative 2θ values because the
diffractometer on ID22 is comprised of a bank of nine detectors spaced at 2o apart. To
ensure that all of them can measure from 0o, scans are started at negative 2θ angles
2.2.3 Gas adsorption measurements:
CO2 gas adsorption measurements were taken at a range of pressures. Each pressure point
represents a series of scans on a different capillary of sample. Below is a table detailing
information about the scans taken. All of the gas adsorption measurements were performed
with two minute scans in the 2θ range -2o to 20o that were translated 1.3 mm every second
scan. All measurements were taken at room temperature.
Table 3. Information on gas adsorption measurements
Sample name CO2 pressure /
bar
Wavelength / Å No. of scans Length of
scans / min
OG10-1 0 0.427654 18 2
0.201 26 2
1.033 27 2
5.214 16 2
OG10-2 0 0.427487 31 2
1.364 40 2
2.271 38 2
5.292 36 2
7.411 36 2
9.977 36 2
12.401 28 2
3. Software
During the placement, the use of several specialised software packages was required. This
section is included to give brief explanations of what each program does. It also includes a
section about various online resources used during the project.
3.1 DASH 3.2 [29]
DASH is a piece of software that has been used for indexing samples during the placement.
Indexing uses peak positions from diffraction patterns to determine a sample’s lattice type
and parameters. This information about unit cells can then be exported into other programs
for further analysis of data. (Indexing can also be done in TOPAS)
3.2 jEdit [30]
jEdit is a java based text editor that is used to create .inp files that are run in TOPAS to
refine a diffraction pattern. It was chosen because there is already an extensive online
community that provides tutorials and plugins for analysis of diffraction data that
facilitates its easy use.
3.3 TOPAS [31]
TOPAS is a program that is used for refinement of diffraction patterns collected on ID22.
It combines information from .xye files which contain the diffraction patterns; and unit cell
parameters taken either from DASH or literature as well as other structural information.
The types of refinement used are explained in section 1.3.1.
3.4 Materials Studio [32]
Materials studio is a modelling program that allows 3D structures to be constructed from
.cif files. There are a number of modules within MS that allow theoretical calculations to
be performed on structures. During the project, the sorption module was used to calculate
theoretical positions of gases adsorbed onto samples. It simulates the adsorption either with
fixed loading or fixed pressure models. Fixed loading determines the preferred binding
sited within a framework for a fixed number of sorbates whereas fixed pressure determines
the amount of sorbate adsorbed at a fixed pressure and temperature. The simulations in
Materials Studio were run using the Metropolis Monte Carlo method which treats the
sorbate (CO2) as a rigid structure and only incorporates rigid body translations and
rotations [23].
3.5 ICSD – Inorganic Crystal Structure Database [33]
The ICSD is an online database containing inorganic crystal structure data which can be
downloaded in .cif format. It has been used to search for structures and impurities
throughout the project.
3.6 CCDC – Cambridge Crystallographic Data Centre [34]
Another online database used for browsing structures. The CCDC also has a collection of
software packages such as Mercury that can be used to model 3D structures and calculate
pore volumes and structures.
4. Results and discussion
4.1 Graph Axes
Unless otherwise stated, the graphs and diffraction patterns presented are in units of square
root of intensity(y axis, arbitrary units) vs. 2θ (x axis, in degrees). The observed diffraction
patterns are shown in black crosses, the calculated pattern in red, the difference curve in
blue and the tick marks in black ‘I’s.
4.2 Radiation Damage Measurements
One of the difficulties faced with using such high energy X-rays for diffraction studies on
ZIF-8 was that it had a very limited lifetime in the beam. The damage was shown by the
drifting and broadening of peaks to higher 2θ angles. Peak drift means that when all the
scans are summed for a particular sample, the peak position is not accurate and the
‘averaged’ peak appears broadened and/or asymmetric. This subsequently results in unit
cell parameters and space groups etc… being calculated incorrectly and affecting the
refinements on the collected diffraction patterns. Peak broadening indicates a reduction in
crystallinity of the sample as the ZIF-8 framework breaks apart in the X-ray beam and long
range order in the crystal is reduced. The extent to which a sample was damaged by the
radiation was dependent on the energy of the X-rays used for collecting PXRD
measurements. As such, a radiation damage test was performed on each sample that used a
different X-ray energy than previous samples. The tests involved a series of fast scans at
the same position to check within which timeframe the shift and broadening occurred. This
allowed the length of scans for a particular sample to be determined and reduce the overall
radiation damage on a sample. The length of scans for the different samples is detailed in
the experimental section.
Figure 8. The same peak of three successive 3 minute scans of OG1 at the same position on a capillary to
show peak shift and broadening. (1st scan in yellow, 2nd in blue and 3rd in green)
4.3 Comparing different synthetic techniques
As alluded to in the experimental section, several different synthetic techniques were used.
This was to find a suitable method to produce ZIF-8 samples with a view to performing gas
adsorption measurements on them. Factors including ease, duration of synthesis and
ecological impact were all considered when choosing a synthetic method as well as the
quality of the diffraction data collected.
4.3.1 DMF (solvothermal) synthesis
This method was chosen as it was already a well reported synthesis [10] and was expected
to yield good quality pure samples of ZIF-8. Some advantages of this synthetic technique
are that it uses near stoichiometric ratios of reagents which reduces waste of the synthesis.
Also, it has been shown to yield highly crystalline samples [11][12] which in turn
improves the quality of PXRD data. However, it tends to be more expensive due to the
costs of the solvent and less ecological as DMF is an organic solvent and hence is more
difficult to dispose of.
It is known from the literature that ZIF-8 has the cubic space group I3m [10].
Sample OG1 was indexed in DASH to give a lattice parameter of 17.032 Å. A Pawley
refinement was then run in TOPAS using the literature space group. As seen in figure 9,
there is generally a good fit between the theoretical and experimental patterns. However,
there are several peaks that aren’t fit at all. This is shown by the difference pattern in blue.
It was therefore suggested that there may be a secondary phase in the sample.
Figure 9. OG1 diffraction pattern with Pawley refinement
It was found that the secondary phase was ZnO. It was found by checking the literature for
likely co products produced in these types of syntheses. The XRD patterns of these
products were checked on the ICSD and visually compared to the experimental patterns.
The impurity was present in all the DMF based samples. ZnO decomposes into water
soluble zinc hydroxides in basic conditions. In an effort to remove the impurity, the DMF
samples were washed with 1 M NaOH and then thoroughly rinsed in deionised water
before drying again. This process didn’t change the composition of the samples and the
impurity remained.
To account for the presence of the impurity in the DMF samples, a ZnO .cif file
[25] was included in the refinement files for DMF based samples. Figure 10 shows the
same Pawley refinement as in figure 9 with the inclusion of the ZnO .cif file. The
remaining peaks were fit which confirmed the presence of the impurity. The inclusion of
the ZnO file reduced the Rwp value from 47.60% to 11.27%.
Figure 10. OG1 Pawley refinement with ZnO .cif file. Lower set of tick marks for ZnO phase
The Rietveld refinement of OG1 used a .cif file of both ZnO and ZIF-8 to fit the
experimental pattern; essentially treating them as two separate phases. Also included in the
Rietveld input file was a Z-matrix of the 2-methylimidazole ring. The refinement gave a
good fit in terms of peak position, however, some of the intensities were not correct and it
gave an Rwp value of just 31.75%.
Figure 11. OG1 Rietveld refinement with ZnO .cif and mIm Z-matrix. Lower set of tick marks for ZnO
phase
One reason that the peak intensities could be off is due to a lack of electron density
in the structure. This could be due to left over solvent or water in the sample, and hence,
subsequent DMF samples were dried for longer or dried under vacuum as detailed in the
experimental section to try and remove it. The good agreement between the experimental
and literature lattice parameters as well as the good Pawley and Rietveld fits means that
it’s reasonable to assume that ZIF-8 has been synthesised.
Subsequent DMF based samples also had well fit patterns and similar lattice
parameters to the literature values which shows that the synthetic method was
reproducible.
Table 4. DMF samples lattice parameters
Sample Rietveld refined lattice parameter / Å
Literature [10] 16.991
OG1 17.032±0.0003
OG4 17.014±0.0002
OG9 17.018±0.0001
OG10-1 17.016±0.0001
OG10-2 17.006±0.0002
4.3.2 Aqueous (hydrothermal) synthesis
Like with the solvothermal methods, this synthetic procedure was chosen as it is well
reported and has been shown to produce ZIF-8 [13]. The main advantage of using this
method is the fact that water is the solvent. Unlike organic solvents, water is easy to
dispose of and doesn’t pose an environmental risk. It is also a very simple synthesis and is
typically performed at relatively low temperatures. However, it can become expensive and
wasteful as most reported syntheses use a large excess of the linker molecule. For this
study, the ratio of zinc nitrate to 2-methylimidazole was reduced to just 1:10 from typical
ratios of 1:70 or 1:100 [13][26].
It was expected that when indexed, these samples would have similar lattice
parameters. However, when OG5 was indexed in DASH, it gave an orthorhombic cell with
the parameters: a=24.071Å, b=19.690Å, c=17.010Å. Also, upon visual comparison of the
diffraction patterns of a DMF sample and OG5, there are clear differences as shown in
figure 12.
Figure 12. OG1 diffraction pattern (DMF)(top), OG5 diffraction pattern (aqueous)(bottom).
A Pawley refinement was run using the lattice parameters generated in DASH and
the space group Cmc21. As shown in figure 13, this refinement gave an extremely good fit
to the experimental OG5 pattern in terms of both peak position and intensity. This is shown
by the relatively flat difference curve (blue) and the low Rwp value of 3.742%. This
strongly suggests that OG5 and the other aqueous samples are single phases.
Figure 13. OG5 Pawley refinement with space group Cmc21
Because the Pawley refinement of OG5 provides such a good fit using the unit cell
parameters and space group from DASH, it cannot be ZIF-8 as it agrees with none of the
literature values.
4.3.3 Ethanol and Acetone (solvothermal) synthesis
This synthesis was chosen as an alternative synthesis to see if changing the solvent to other
small organic molecules had any effect on the product produced or its crystallinity. As with
the other syntheses, it has the advantage of being a simple synthesis that is quick and easy
to perform.
Both OG7 (ethanol) and OG8 (acetone) were indexed to give the space group I3m
and the lattice parameters of a=16.991Å and a=16.954Å respectively. This was a good first
indication that these syntheses had both yielded ZIF-8. To further confirm this, a Pawley
refinement was performed on both diffraction patterns as shown below in figure 14.
Figure 14. OG7 Pawley refinement (top) and OG8 Pawley refinement (bottom)
Both diffraction patterns have extremely good Pawley fits with Rwp values of
3.034% (OG7) and 2.773% (OG8) and do not show any reflections of the ZnO impurity
observed in the DMF samples. However, the peaks are much broader and particularly at
higher 2θ angles, most peaks aren’t resolved at all. This shows that these samples have a
lower degree of crystallinity than either the aqueous or DMF based samples which both
have very sharp peaks.
Rietveld refinements that gave better fits than the DMF samples in terms of peak
intensity were also run on OG7 and OG8 as another confirmation that ZIF-8 had been
produced. As with the Pawley refinements, good fits were obtained for both samples
shown by figure 15. However, particularly with OG8, the very broad peaks in the
diffraction pattern make it difficult to fit the less intense ones. This is shown by the slightly
wavy difference curve in blue.
Figure 15. OG7 Rietveld refinement: Rwp=8.168% (top), OG8 Rietveld refinement: Rwp=6.681% (bottom)
4.3.4 Choosing a synthesis for gas adsorption measurements
It was important to choose the most appropriate samples for gas adsorption. Ideally, the
experimental lattice parameter, space group, unit cell volume etc. should all be concurrent
with the literature values. These values should be taken from well fit refinements to ensure
they’re as accurate as possible.
Table 5. Comparison of certain values from different synthetic techniques vs. literature values. *Rietveld
refined
Synthetic
method
Space group Lattice
parameter* / Å
Unit cell
volume / Å3
Rietveld Rwp /
%
Literature [10] I3m a=16.991 4905 n/a
DMF (OG10-
2) I3m a=17.006±0.0002 4918±0.268 14.669
Aqueous
(OG5)
Cmc21 a=24.071±0.0003,
b=19.690±0.0006,
c=17.010±0.0004
8062±1.043 3.742 (Pawley)
Ethanol (OG7) I3m a=16.585±0.0006 4562±0.493 8.168
Acetone (OG8) I3m a=16.631±0.001 4600±0.923 6.681
Table 5 shows that there is an obvious outsider amongst the syntheses. The aqueous
synthesis does not have anything in common with the literature values. As mentioned in
section 4.5.2, the samples are not ZIF-8 which is shown by the very different lattice
parameters and different lattice type. So for the purposes of gas adsorption experiments, it
was excluded. It is revisited as a separate section in the appendix.
The other three syntheses were more difficult to choose between. They all have the
correct space group for ZIF-8 and the lattice parameters are fairly close. Arguably, the
lattice parameters for the ethanol and acetone samples are too small which is also reflected
in their smaller unit cell volumes. The major disadvantage of the ethanol and acetone
syntheses is the broadness of their peaks. The reason this is a disadvantage is because the
position of the peaks give vital information about the crystal such as the lattice parameter.
When gas adsorption measurements are made, a key indication that gas has been adsorbed
into the pores of the framework is peaks moving to lower 2θ angles. This shows an
expansion of the unit cell (i.e. bigger lattice parameter as gas is adsorbed). Therefore, if the
peaks are broad, it is more difficult to accurately measure the position of the peaks, and
hence the unit cell can be calculated less accurately.
Taking the above into account, it was decided that the DMF based samples were
the most appropriate to use for gas adsorption measurements. This was because, despite the
fact that there was an impurity in the DMF samples (which would only act as a spectator
molecule and hence not interfere with the ZIF-8 chemistry), their high degree of
crystallinity (as indicated by their very sharp intense peaks) and concurrence with literature
data on ZIF-8, was preferable to the broad inaccurate peaks of the other samples.
4.4 Gas adsorption measurements
With the prevalence of issues like global warming and dwindling fossil fuel supplies
demanding a need for ever more efficient and green ways to separate and store gases, ZIFs
have received much interest [35]. The fact that ZIFs are highly porous and possess
tuneable pore sizes as well as a range of structures, makes them an attractive class of
compounds for selective gas separation and gas storage.
In particular, ZIF-8 has generated a lot of interest in gas separation as it has a small
pore aperture of 0.34nm [17]. This could make ZIF-8 useful in the separation of small
molecules like hydrogen and carbon dioxide from other small molecules including some
small hydrocarbons as well as storage of these small molecules.
This lead to the decision that CO2 was to be used for adsorption measurements on
the DMF samples of ZIF-8. Specifically OG10-1 and OG10-2. The aim of these
measurements were to try and determine the position of CO2 molecules once within the
pores of the framework.
4.4.1 Lattice parameter vs. pressure for OG10-1 and OG10-2 in-situ gas adsorption
measurements
As detailed in the experimental section, PXRD measurements were run at a range of
pressures with each pressure point corresponding to a separate capillary. The first capillary
at zero bar was evacuated overnight prior to the measurement in an effort to remove
anything within the pores, however the other capillaries were only pumped for 30 minutes
prior to taking the measurements.
Like with OG10-1, one capillary of OG10-2 was used for each pressure point
measured. However, unlike OG10-1, all the OG10-2 were evacuated for the same amount
of time before the measurements were made. The details of which are found in section
2.1.1. This was to try and ensure that all the samples were directly comparable as with
OG10-1, the empty sample appeared to be an anomaly.
Rietveld refinements were run on each of the pressure points (some details of
which can be found in tables A3 and A4 of the appendix) and yielded good fits concurrent
with the space group of ZIF-8. As expected for an adsorption process, the lattice
parameters increased with increasing pressure shown by figure 16.
Figure 16. Plot to show OG10-1 and OG10-2 Rietveld lattice parameters vs. CO2 pressure in bar. Trendline
included only as a guide for the eye
Figure 16 shows the trend for OG10-1 that lattice parameter increases with
increasing pressure. However, there is one noticeable anomaly: The evacuated sample at
zero bar for OG10-1 has a lattice parameter larger than expected. This could be due to the
capillary not being properly sealed causing a leak in the system and thus preventing
evacuation of the sample. A second series of measurements were made on OG10-2 to try
and avoid this anomaly and to obtain a larger range of pressure points.
17
17.01
17.02
17.03
17.04
17.05
17.06
0 2 4 6 8 10 12 14
Latt
ice
par
amet
er /
Å
CO2 Pressure / bar
Lattice parameter vs. pressure for OG10-1 and OG10-2
OG10-1 OG10-2
As with OG10-1, these followed the trend of increasing lattice parameter with
increasing pressure of CO2. However, the sample at zero bar with no gas loading is not an
outlier. Further, it is notable that the trendline starts to level off at higher pressures. This
suggests that there will be a maximum lattice parameter that the unit cell can stretch to.
This is likely to be reached when the pore is fully saturated with CO2.
4.4.2 Modelling of ZIF-8 and its pore structure
The refined structure models were exported as a .cif file from TOPAS for further
modelling in Materials Studio and Mercury 3.5. As well as providing a 3D representation
of the pores of the framework, Mercury allows the pore volume and their percentage of the
unit cell to be calculated. These values can be found for both OG10-1 and OG10-2 in
tables A3 and A4 of the appendix. The values for the evacuated sample of OG10-1 and
OG10-2 are in good agreement with the literature values [10]. Figures 17 and 18 show the
structure and pore structure of both samples.
Figure 17. OG10-1 evacuated structure from .cif in Materials Studio (left), OG10-1 evacuated structure
showing pore structure in yellow in Mercury 3.5 (right). White hexagon used to show pore opening on the
left structure
Figure 18. OG10-2 evacuated structure in Materials Studio (left), OG10-2 evacuated structure in Mercury
3.5 showing pore structure in yellow (right). White square used to show pore opening on the left structure
The left hand structure in figures 17 and 18 show that the ZIF-8 framework appears
to have large hexagonal and smaller square pore openings present. However, when the
internal pore surfaces were calculated in Mercury 3.5 (as shown by the right hand
structures); it appears that the pores are only accessible by the larger hexagonal openings.
These internal pore surfaces were calculated by rolling a spherical probe of 1.2 Å around
the unit cell to find the edges of the pore. These calculations show that the square pore
openings are likely to be too small for access to the pore. Park et al. [10] have calculated
the diameter of the hexagonal opening to be ~3.4 Å which is large enough to facilitate the
adsorption of CO2.
4.4.3 CO2 gas location
From the increase in lattice parameter with increased gas pressure, we can be confident
that CO2 was adsorbed into the pores of the ZIF-8 samples. The next stage of analysis was
to try and locate the CO2 molecules once within the pores. This was to see whether it could
give any information on the mechanism of adsorption. This was done using Fourier
difference maps. These maps show the electron density of anything within the pores by
showing the difference between the experimental (with gas) and calculated (without gas)
structure of the framework. Figures 19 and 20 how the Fourier difference maps for OG10-
1 and OG10-2 at the different pressures measured (excluding zero bar as no gas should be
present in the pores).
Figure 19. Fourier Difference maps for OG10-1: a) 0.2 bar, b) 1 bar, c) 5 bar. Electron density clouds in
red/yellow (yellow signifies greater intensity)
A) B)
C)
Figure 20. Fourier difference maps for OG10-2: a) 1 bar, b) 2 bar, c) 5 bar, d) 7.5 bar, e) 10 bar, f) 12.5 bar
Although slightly difficult to see, there is a relatively diffuse cloud in the centre of
the pore at all the pressures but no apparent pockets of intense electron density. It is likely
that this cloud represents the CO2 molecules that have been adsorbed but could also be due
to any solvent or water that remained in the pore. This shows that for both samples, the
adsorption of CO2 is probably occurred via the same mechanism.
4.4.4 Theoretical gas loading simulations
To support the empirically derived calculations in the previous sections, calculations were
performed in Materials Studio to try and determine the theoretical position of CO2
molecules within the pores of ZIF-8. Framework models for ZIF-8 were produced for
every pressure point for OG10-1 and OG10-2. This was done using the fixed pressure
model of the sorption module in Materials Studio as described in section 3.4. Figures 21
and 22 show the frameworks with CO2 molecules in the pores.
A) B) C)
D) E) F)
A) B)
Figure 20. Fixed pressure adsorption calculations for OG10-1 from Materials Studio: a) 0.2 bar, b) 1 bar, c) 5
bar. CO2 molecules represented by ball and stick models
Figure 21. Fixed pressure adsorption calculations for OG10-2 from Materials Studio: a) 1 bar, b) 2 bar, c) 5
bar, d) 7.5 bar, e) 10 bar, f) 12.5 bar
As shown in figures 20 and 21, the number of CO2 molecules that are calculated to be
adsorbed does increase with increasing pressure. However, these calculations do not seem
to indicate a preferential location of CO2 within the pores, similar to the Fourier difference
maps (figures 19 and 20).
C)
A) B)
C) D)
E) F)
The theoretical calculations also allowed us to determine the average loading of the
unit cell. This provided a useful quantitative look at the loading of CO2 onto ZIF-8. The
results of these average loading calculations are shown in tables 6 and 7.
Table 6. Theoretical average CO2 loading on OG10-1 samples
Pressure / bar Average loading / no. of CO2 molecules
per unit cell
0.2 2
1.0 5
5.2 15
Table 7. Theoretical average CO2 loading on OG10-2 samples
Pressure / bar Average loading / no. of CO2 molecules
per unit cell
1.36 5
2.27 9
5.29 14
7.41 16
9.97 18
12.40 19
The Fourier difference maps, the Materials studio simulations, the average loading
calculations and the increasing lattice parameters for both samples show that the amount of
gas adsorbed increased with increasing pressure. It has been shown that there are no
specific gas positions once CO2 has been adsorbed into the pores of the ZIF-8 samples.
This isn’t entirely surprising for a neutral molecule such as CO2 with only small dipoles on
the CO bonds. This coupled with the fact that the Zn atoms within the framework have no
free coordination sites, implies that the predominant interactions occurring between the gas
molecules and the framework are Van der Waals forces.
5. Conclusion
The experiments conducted show that ZIF-8 can be synthesised in a variety of ways. The
methods tried in this study are just a few of the methods that can easily produce ZIF-8.
Both the DMF based and ethanol/acetone based methods successfully produced ZIF-8.
This was confirmed by indexing and refinement of the samples giving the correct space
group (I3m) and lattice parameter (a=~17Å) as stated in the literature [10].
For the aqueous based samples that did not produce ZIF-8, it could have been due
to the solvent used (i.e. water). Tan and Nordin have both suggested that DMF and
additives like triethylamine could be acting as structure directing agents and giving the
framework a support to form around [27][28]. As mentioned in the results and discussion
section, the aqueous samples are referred to in the appendix in greater detail.
Whilst the other two syntheses successfully produced ZIF-8, they were not without
their flaws. The ethanol and acetone synthesis produced pure ZIF-8 but had poor
crystallinity as indicated by broad, low intensity peaks. The DMF synthesis produced
highly crystalline ZIF-8 but contained an impurity. It also appeared that some DMF
remained in the pores, even after evacuation. This was an issue that was also noted in the
literature [10]. In the future, it would be worth investigating solvent exchanges in addition
to evacuation to try and completely remove the DMF before gas adsorption measurements.
It would be useful to couple PXRD with some other techniques. For example, IR
spectroscopy would be useful to determine if solvent remained in the pores when using
organic solvents like those used in this study. Elemental analysis and single crystal
measurements would further support the confirmation that ZIF-8 had been produced.
The CO2 adsorption measurements showed that the gas can be readily adsorbed into
the pores of ZIF-8 via hexagonal pore openings. This was illustrated by the lattice
parameter increasing as the pressure of gas loaded onto the sample increased. The Fourier
difference maps gave a visual representation of the electron density from the CO2
molecules within the pores of the framework. However, they have their limitations as it
likely that some DMF remained in the pores which would have also been shown in the
Fourier maps, hence altering their appearance. The Fourier maps were also used to try and
identify any specific CO2 adsorption sites in the framework which would have been shown
by more intense pockets of electron density. Because the electron density within the pores
appeared to be diffuse, it is likely that there are not any specific binding sites for CO2 and
that any interaction between the gas molecules and the framework will be just Van der
Waals interactions.
The theoretical calculations performed in Materials Studio and Mercury offered a
useful method of comparison between them and the experimental structures and Fourier
Maps. They supported the empirical data and suggested that there were no specific
adsorption sites for CO2 molecules. The average loading calculations supported the fact
that the unit cell expanded upon loading with CO2. However, as these calculations are
theoretical, their outcome is only as good or accurate as the model used to perform them.
It would be interesting to perform further gas adsorption experiments using
different gases. For example, as an inert monoatomic gas, such as Kr would be relatively
simple to model and would have the advantage of having very little interaction with the
framework. This may make it effective in determining further information about the pore
structure and capacity.
It has been speculated that ZIF-8 would be a good candidate for gas storage and
separation. However, from the adsorption measurements performed in this study, it was
apparent that while ZIF-8 readily adsorbed the gas, there was nothing to stop it simply
escaping the pores. This suggests that ZIF-8 would not be suitable for storage of CO2. It
may be more suitable for gas separation of small organic molecules including some
industrially relevant small hydrocarbons especially if ZIF-8 thin films can be produced.
This is due to the pore aperture being a similar size to certain small organic molecules [9].
This could be tested by passing gas mixtures through the sample and analysing the
composition of the gas that is expelled.
Acknowledgements
Many thanks to my supervisors Christina Drathen and Andy Fitch as well as the rest of the
staff on ID22 for all their help and for making my year in Grenoble so rewarding.
References
1. Introduction to the ESRF for Journalists [online]; Available from: http://www.esrf.eu/about/press-
room/intro-esrf-journalists [Accessed on 01/04/15]
2. ESRF quick facts for journalists [online]; Available from: http://www.esrf.eu/about/press-
room/quick-facts [Accessed on 01/04/15]
3. Synchrotrons [online]; Available from: http://www.esrf.fr/UsersAndScience/Links/Synchrotrons
[Accessed 01/04/15]
4. Research with synchrotron X-rays boosts industrial innovation [online]; Available from:
http://www.esrf.fr/news/general/industrycollaborationsurvey/index_html [Accessed on 01/04/15]
5. Services [online]; Available from: http://www.esrf.eu/about/services [Accessed on 01/04/15]
6. Structure of materials [online]; Available from:
http://www.esrf.fr/UsersAndScience/Experiments/StructMaterials/ [Accessed on 01/04/15]
7. Science at ID22 [online]; Available from: http://www.esrf.fr/id22/science [Accessed on 01/04/15]
8. O.M. Yaghi, G. Li, H. Li; Nature; 1995; vol. 378; 703-706
9. J.R. Li, R.J. Kuppler, H.C. Zhou; Chemical Society Reviews; 2009, vol. 38, 1477-1504
10. K.S. Park, Z. Ni, A.P. Côté, J.Y. Choi, R. Huang, F.J. Uribe-Romo, H.K. Chae, M. O’Keeffe, O.M.
Yaghi; Proceedings of the National Academy of Sciences of the United States of America; 2006; vol.
103 no. 27; 10186-10191
11. E.L. Bustamante, J.L. Fernández, J.M. Zamaro; Journal of Colloid and Interface Science; 2014; vol.
424; 37-43
12. S.R. Venna, J.B. Jasinski, M.A. Carreon; Journal of the American Chemical Society; 2010; vol. 132
no. 51, 18030-18033
13. K. Kida, M. Okita, K. Fujita, S. Tanaka, Y. Miyake; CrystEngComm; 2013, vol. 15 no. 9; 1794-
1801
14. B. Chen, Z. Yang, Y. Zhu, Y. Xia; Journal of Materials Chemistry A; 2014; vol. 2 no. 40; 16811-
16831
15. A. Phan, C.J. Doonan, F.J. Uribe-Romo, C.B. Knobler, M. O’Keeffe, O.M. Yaghi; Accounts of
Chemical Research; 2010, vol. 43, 58-67
16. J. Cravillon, S. Münzer, S. Lohmeier, A. Feldhoff, K. Huber, M. Wiebcke; Chemistry of Materials;
2009; vol. 21 no. 8, 1410-1412
17. D. Fairen-Jiminez, S.A. Moggach, M.T. Wharmby, P.A. Wright, S. Parsons, T. Düren; Journal of
the American Chemical Society; 2011, vol. 133 no. 23; 8900-8902
18. S.B. Kalidindi, D. Esken, R.A. Fischer; Chemistry a European Journal; 2011; vol. 17; 6594-6597
19. P. Atkins, J. De Paula; Atkins’ Physical Chemistry; OUP, Oxford, Ninth edn., 2010, 696-704
20. What is a synchrotron? [online]; Available from: http://www.esrf.fr/about/synchrotron-
science/synchrotron [Accessed on 23/04/15]
21. ID22 [online]; Available from:
http://www.esrf.fr/home/UsersAndScience/Experiments/Beamlines/content/content/ID22.html
[Accessed on 23/04/15]
22. Technical description [online]; Available from: http://www.esrf.fr/id22/technical-description
[Accessed on 24/04/15]
23. Sorption Datasheet, Accelrys [online]; Available from:
http://accelrys.com/products/datasheets/sorption.pdf [Accessed on 19/05/15]
24. B.H. Toby; Powder Diffraction; 2006; vol. 21 no.1; 67-70
25. S.C Abrahams, J.L Bernstein; Acta Crystallographica B; 1969; vol. B25; 1233-1236
26. Y. Pan, Y. Liu, G. Zeng, L. Zhao, Z. Lai; Chemical Communications; 2011, vol. 47; 2071-2073
27. J.C. Tan, T.D. Bennett, A.K. Cheetham; Proceedings of the National Academy of Sciences of the
United States of America; 2010; vol. 107 no. 22; 9938-9943
28. N.A.H.M. Nordin, A.F. Ismail, A. Mustafa, P.S. Goh, D. Rana, T. Matsuura; RSC Advances; 2014;
vol. 4; 33292-33300
29. W.I.F. David, K. Shankland, J. van de Streek, E. Pidock, W.D.S. Motherwell, J.C. Cole; Journal of
Applied Crystallography; 2006; vol. 39; 910-915
30. jEdit version 4.3.1 [Computer software]; 2014; Available from: www.jedit.org [Accesed on
25/07/14]
31. TOPAS version 5 [Computer software]; 2014; Available from: www.bruker-axs.com
32. Materials Studio version 6.1.2 [Computer software]; 2012; Available from:
http://accelrys.com/products/materials-studio/quantum-and-catalysis-software.html
33. Inorganic Crystal Structure Database [online]; Available from: http://www.fiz-
karlsruhe.de/icsd_web.html
34. Cambridge Crystallographic Data Centre; Available from:
http://www.ccdc.cam.ac.uk/pages/Home.aspx
35. B. Chen, Z. Yang, Y. Zhu, Y. Xia; Journal of Materials Chemistry A; 2014; vol. 2 no. 40; 16811-
16831
Appendix A1. Z-Matrix coordinates
A1.1 mIm:
The third column is the bond distance between the sites in the first two columns; the fifth
column is the bond angle between the sites in columns two and four; the final column is
the torsion angle between the sites in columns four and six.
C1b
N1b C1b 1.3970
C2b N1b 1.3684 C1b 108
C3b C1b 1.5283 N1b 120 C2b 180
H1b C2b 0.9330 N1b 120 C1b 180
H5b C3b 0.9631 C1b 109.5 N1b 0
H6b C3b 0.9631 C1b 109.5 H5b 120
H7b C3b 0.9631 C1b 109.5 H6b 120
A2. Atomic coordinates
X,y,z represent fractional unit cell coordinates
Num_posns represents the relative number of each atom within each unit cell
A2.1 ZIF-8: Table A1. Atomic coordinates of ZIF-8
Site x y z Num_posns
C1b c1x 0.37790 1.00968 =1-c1x;: 0.60978 24
C2b 0.36902 0.89931 0.68083 48
C3b c3x 0.40829 1.09209 =1-c3x;: 0.59075 24
H1b 0.38002 0.86525 0.72241 48
H5b 0.44490 1.10843 0.63075 48
H6b 0.43434 1.09148 0.54047 48
H7b 0.36482 1.12834 0.58903 48
Zn1b 0.5000 1.0000 0.7500 12
N1b 0.40473 0.97133 0.67729 48
A2.2 ZnO: Table A2. Atomic coordinates of ZnO
Site x y z
Zn1 1/3 2/3 0
O1 1/3 1/2 0.3825
A3. Crystallographic data:
A3.1 OG10-1 with CO2 adsorption:
Table A3. Various crystallographic data on OG10-1
Empty 0.2 Bar 1 Bar 5 Bar
Space group I3m I3m I3m I3m
Lattice
parameter / Å 17.016 17.006 17.015 17.027
Pore volume /
Å3 2388 2383 2387 2392
Percentage of
unit cell* / % 48.5 48.5 48.5 48.5
Rietveld Rwp
value / % 12.016 7.223 10.392 11.155
*Literature value = 47.6%
A3.2 OG10-2 with CO2 adsorption:
Table A4. Various crystallographic data on OG10-2
Empty 1 Bar 2 Bar 5 Bar 7.5 Bar 10 Bar 12.5 Bar
Space
group I3m I3m I3m I3m I3m I3m I3m
Lattice
parameter
/ Å 17.006 17.012 17.018 17.034 17.043 17.049 17.055
Pore
volume / Å3 2384 2386 2388 2395 2399 2401 2420
Percentage
of unit cell
/ % 48.5 48.5 48.5 48.5 48.5 48.5 48.5
Rietveld
Rwp value /
% 14.667 16.205 16.639 19.384 20.061 20.789 21.039
*Literature value = 47.6%
A4. Diffraction experiment details
A4.1 Preparing capillaries:
For diffraction measurements that involved no gas loading, borosilicate glass capillaries
with a diameter of 1mm were filled with sample. The capillaries were then sealed by
passing through a blowtorch. Finally, they were mounted into brass capillary holders and
held in place by wax.
When gas loading was involved, quartz glass capillaries were used as they have
greater resistance to pressure. The samples were held in place by pushing glass wool down
the capillary but they weren’t sealed so they could be loaded with gas. The capillaries were
then glued into brass holders with epoxy glue.
Figure 1. Sample in borosilicate capillary
Figure 2. Sample in quartz capillary mounted on goniometer head for gas adsorption measurements
A4.2 The gas rig:
The gas rig allows a fixed amount of gas to be loaded onto a sample. It also allows a
sample to be evacuated prior to loading the gas in an effort to remove any solvent and dry
the sample as much as possible.
Figure 3. The gas rig at ID22
A5. Aqueous Syntheses
This section is included in the appendix as it is ongoing and will be the main focus of my
work for my remaining months at the ESRF. Below is a very brief summary of what has
been done to try and solve the structure of hydrothermally synthesised samples of ZIF-8 so
far.
As mentioned in the results and discussion section in the main report, the samples
produced using the aqueous synthetic method didn’t yield ZIF-8. This leaves the question
of what was produced, as the reagents were the same as in the other synthetic methods. The
only real difference was the solvent used. A series of computer based techniques have
been used to try and determine the structure of OG5.
A5.1 Indexing
Indexing of the aqueous samples’ diffraction patterns was carried out in TOPAS to
determine their lattice parameters and space groups. It was found that the samples had an
orthorhombic unit cell with lattice parameters: a=24.057 Å, b=19.673 Å, c=16.983 Å.
Initially, the space group suggested was Cmc21.
A5.2 Pawley refinements
Pawley refinements were run in TOPAS using the space group generated in the indexing
stage as well as other space groups that follow group relationships as found in the
international tables of crystallography. The idea was to find the space group with the
highest symmetry that fit all the peaks. The unit cell axes were swapped around in an effort
to find a better fit (i.e. abc, acb, bac etc). It was found that the space group that provided
the best fit was Cmca and the lattice parameters were refined to: a=24.059 Å, b=16.965 Å,
c=19.675 Å. The Pawley refinements were run using the largest possible 2θ range to
improve statistics.
A5.3 Charge flipping
Charge flipping is a method used in the determination of unknown structures from a
Pawley refinement fit and are also run in TOPAS. It produces an electron density map
similar to Fourier difference maps. It is then possible to ‘pick atoms’ from the electron
density plot. Likely atom positions will be in the spots where the intensity of electron
density is located with heavier atoms obviously in the most intense areas.
It is an appealing method for structure determination as it requires no information
on atom types or chemical composition. Charge flipping works particularly well on data
with good resolution (<1 Å) which makes the data collected on ID22 suitable for the
technique.