A Porous Cobalt Tetraphosphonate Metal–Organic Framework: Accurate Structure and Guest Molecule Location Determined by Continuous-Rotation Electron Diffraction

Article abstract of DOI:10.1002/chem.201804133

Single-crystal electron diffraction has shown to be powerful for structure determination of nano- and submicron-sized crystals that are too small to be studied by single-crystal X-ray diffraction. However, it has been very challenging to obtain high quality electron diffraction data from beam sensitive crystals such as metal–organic frameworks (MOFs). It is even more difficult to locate guest species in the pores of MOF crystals. Here, we present synthesis of a novel porous cobalt MOF with 1D channels, [Co₂(Ni-H₄TPPP)]?2 DABCO?6 H₂O, (denoted Co-CAU-36; DABCO=1,4-diazabicyclo[2.2.2]octane), and its structure determination using continuous rotation electron diffraction (cRED) data. By combining a fast hybrid electron detector with low sample temperature (96 K), high resolution (0.83–1.00 ?) cRED data could be obtained from eight Co-CAU-36 crystals. Independent structure determinations were conducted using each of the eight cRED datasets. We show that all atoms in the MOF framework could be located. More importantly, we demonstrate for the first time that organic molecules in the pores, which were previously difficult to find, could be located using the cRED data. A comparison of eight independent structure determinations using different datasets shows that structural models differ only on average by 0.03(2) ? for the framework atoms and 0.10(6) and 0.16(12) ? for DABCO and water molecules, respectively.

Full text of DOI:10.1002/chem.201804133

A Journal of
Accepted Article
Title: A porous cobalt tetraphosphonate metal-organic framework:
accurate structure and guest molecule location determined by
continuous rotation electron diffraction
Authors: Bin Wang, Timo Rhauderwiek, Andrew Kentaro Inge, Hongyi
Xu, Taimin Yang, Zhehao Huang, Norbert Stock, and
Xiaodong Zou
This manuscript has been accepted after peer review and appears as an
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of the final Version of Record (VoR). This work is currently citable by
using the Digital Object Identifier (DOI) given below. The VoR will be
published online in Early View as soon as possible and may be different
to this Accepted Article as a result of editing. Readers should obtain
the VoR from the journal website shown below when it is published
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content of this Accepted Article.
To be cited as: Chem. Eur. J. 10.1002/chem.201804133
Link to VoR: http://dx.doi.org/10.1002/chem.201804133
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10.1002/chem.201804133
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A porous cobalt tetraphosphonate metal-organic framework:
accurate structure and guest molecule location determined by
continuous rotation electron diffraction
Bin Wang,[a] ‡ Timo Rhauderwiek,[b] ‡ A. Ken Inge,[a] Hongyi Xu,[a] Taimin Yang,[a] Zhehao Huang,[a]
Norbert Stock,*[b] and Xiaodong Zou*[a]
Abstract: Single crystal electron diffraction has shown to be powerful
for structure determination of nano- and submicron-sized crystals that
are too small to be studied by single crystal X-ray diffraction. However,
it has been very challenging to obtain high quality electron diffraction
data from beam sensitive crystals such as metal-organic frameworks
(MOFs). It is even more difficult to locate guest species in the pores
of MOF crystals. Here we present synthesis of a novel porous cobalt
In order to establish structure-property relationships,
structure determination of new MOFs is of paramount
importance. The most conventional technique, single crystal
X-ray diffraction, is not applicable to many MOFs because
they are only obtained as nano- or micrometer-sized crystals.
Electron crystallography, especially the recent emergence of
the rotation method in electron diffraction, such as
Automated Diffraction Tomography (ADT)[17] and Rotation
Electron Diffraction (RED),[18,19] has shown to be powerful for
structure solution of such small crystallites.[20] One of the
major drawbacks of electron crystallography on MOFs has
been electron beam damage of the crystals. The beam
damage often results in a reduction of data resolution and
completeness, which prevents determination of accurate
structural models and location of guest molecules in the
pores. It is often necessary to perform Rietveld refinement
using powder X-ray diffraction (PXRD) in order to obtain the
detailed structural information.[21,22] However, it is not always
possible to obtain high quality PXRD data needed for
Rietveld refinement. Therefore, it is of significant interest to
minimize electron beam damage in the data collection so that
high quality electron diffraction data can be obtained for
accurate structure determination.
MOF with 1D channels, [CO2(NI-H4TPPP)]∙2DABCO∙6H2O, (denoted
CO-CAU-36),
and its structure determination using continuous
rotation electron diffraction (cRED) data. By combining a fast hybrid
electron detector with low sample temperature (96 K), high resolution
(0.83 – 1.0 Å) cRED data could be obtained from eight Co-CAU-36
crystals. Independent structure determinations were conducted using
each of the eight cRED datasets. We show that all atoms in the MOF
framework could be located. More importantly we demonstrate for the
first time that organic molecules in the pores, which were previously
difficult to find, could be located using the cRED data. A comparison
of eight independent structure determinations using different datasets
shows that structural models differ only on average by 0.03(2) Å for
the framework atoms and 0.10(6) and 0.16(12) Å for water and
DABCO molecules, respectively.
Metal-organic frameworks (MOFs) are an intensively
investigated class of materials. Due to their modular
structures, the pore size and pore surface properties can be
tuned, which in turn lead to a large range of chemical and
physical properties.[1–4] MOFs have shown wide applications
such as gas storage and separation, drug delivery and
catalysis.[1,3,5–7] While most porphyrin-based MOFs have
been obtained using tetracarboxyporphyrin (H6TCPP) as the
The data collection in the original ADT and RED methods is
performed in a stepwise manner, where the crystal is rotated
in a discrete step to a given angle before an ED pattern is
taken.[17–19] A complete data collection normally takes 1-2
hours. A much faster data collection has been achieved by
continuously rotating the crystal during data collection.[23,24]
Unlike the stepwise RED (sRED), each ED frame in the
continuous rotation electron diffraction (cRED) data records
integrated intensities of reflections within a given rotation
interval (Fig. S6). Using a recently installed fast and noise-
free hybrid electron counting detector, the data collection
time can be shortened to 0.5-4 min for a typical cRED dataset.
In addition, the low background of the detector makes it
possible to detect weak reflections at high scattering angles.
In combination with sample cooling (< 100 K), beam damage
is greatly reduced and data resolution is enhanced.[25]
linker,
only
two
with
the
Ni-(4-
tetraphosphonophenylporphyrin) (Ni-H8TPPP) linker have
been reported.[8,9] This observation is in line with the fewer
number of known porous metal phosphonates in comparison
to porous metal carboxylates.[10,11] In terms of cobalt MOFs,
only four porous cobalt phosphonate-based MOFs are
currently known.[12–16]
Here we report the synthesis and ab initio structure
determination of a new cobalt phosphonate with permanent
porosity, denoted Co-CAU-36. Using eight high resolution
cRED datasets collected at 96 K from different crystals, we
demonstrate that a complete structure determination can be
achieved using cRED data, and the structure solution and
refinement procedures with cRED data are similar to those
with single crystal X-ray diffraction. We show that precise
structural models can be obtained from each of the eight
datasets. We are able to not only determine the framework
[a]
Bin Wang, A. Ken Inge, Hongyi Xu, Taimin Yang, Zhehao Huang
and Xiaodong Zou
Department of Materials and Environmental Chemistry,
Stockholm University,
SE-106 91 Stockholm, Sweden
E-mail: xzou@mmk.su.se
Timo Rhauderwiek and Norbert Stock
Institut für Anorganische Chemie,
Christian-Albrechts-Universität zu Kiel,
DE-24118 Kiel, Germany
[b]
[‡]
E-mail: stock@ac.uni-kiel.de
These authors contributed equally to this work.
Supporting information for this article is given via a link at the end of
the document
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structure of the MOF, but also for the first time locate and
refine the guest molecules in the pores.
Structure refinement was subsequently performed against cRED
data using SHELXL[32] assuming kinematical intensities. All non-
hydrogen framework atoms and water molecules were refined
without applying any geometrical restraints. Soft restraints were
applied to the DABCO molecule. The final R1 value converged to
0.1356 for 1978 unique reflections with F2 > 2σ(F2) and 0.2133 for
all 4008 unique reflections. The relatively high R-values
compared to those in X-ray crystallography are due to the
presence of dynamical effects and other errors in electron
diffraction intensities.[33] The data collection, crystal data and
refinement details are given in Table 1 and Section S3, ESI. Due
to the fast data collection and high data quality, the entire
structure determination process was accomplished within 9 hours,
including TEM sample preparation, data collection, structure
solution and refinement. The final refined chemical formula of Co-
CAU-36 is [Co2(Ni-H4TPPP)]·2DABCO·6H2O.
The crystal structure of Co-CAU-36 is shown in Figure 2b-d. The
framework structure contains one cobalt, one nickel, one
phosphorus, and three oxygen atoms in the asymmetric unit.
The cobalt atom is coordinated by four oxygen atoms from four
different phosphonate groups, one from each Ni-H4TPPP4-
moiety, to form 1D chains along [001] with alternating CoO4 and
PO3C tetrahedra (Figure 2c). The bond distances are 1.94(2)-
1.97(2) Å for Co-O, 1.53 (2) -1.57(2) Å for P-O and 1.84(2) Å for
P-C, and the bond angles are 103.6(6)-119.4(10)° for O-Co-O
and 105.2(8)-113.4(9)° for O-P-O(C). This structural motif has
been previously described[34] and in CoCAU-36 the chains are
connected through the porphyrin Ni-H4TPPP4- moieties to form
a 3D framework containing 1D channels. This results in a pore
diameter of ca. 9 Å taking the DABCO guest molecules into
account and a diameter of ca. 12.5 Å when the pores are empty
(Figure 2b, Figure S8). The distance between the Ni ions in the
porphyrin centers is 4.48 Å. The water molecules (Ow1, Ow2),
together with the terminal hydroxyl group of the PO3C tetrahedra
(O3), form a strong H-bonding network (Figure 2d, O3…Ow1 =
2.60 Å and Ow1…Ow2 = 2.81 Å). The DABCO molecule also
forms H-bond with the framework (N3…O3 = 2.82 Å).
The synthesis and characterization of the linker Ni-H8TPPP are
given in the Supporting Information (Figures S1-S4). Co-CAU-36
was synthesized in the system Co2+/Ni-H8TPPP/DABCO/HCl in
water at 140 °C. A systematic investigation for optimization of the
synthesis parameters was carried out using high-throughput (HT)
methods.[26–28] The results of the HT investigation are illustrated
in Figure S5. The product formation depends mainly on the
amount of DABCO and the linker to metal ratio. A highly
crystalline product of Co-CAU-36 was obtained using the molar
ratios of Co2+ : Ni-H8TPPP : DABCO : HCl = 1 : 1 : 50 : 4.
SEM images show that crystals of Co-CAU-36 have a rod-
like morphology with diameters of less than 1 μm (Figure 1a).
Due to the small crystal sizes, the structure determination of
Co-CAU-36 was conducted using continuous rotation
electron diffraction (cRED) data. Eight individual datasets
were collected at 96 K using a cooling sample holder. Unit
cell parameters were determined from one single cRED
dataset to be a = 22.17, b = 21.91, c = 9.06 Å, α = 90.05, β
= 90.66 and γ = 91.58°, which were reasonably close to a
tetragonal cell. The cRED data was further processed and
intensities were extracted using the software XDS.[29] The
unit cell parameters were refined in a tetragonal cell against
the cRED data using XDS (a = 21.980(5), c = 8.960(2) Å),
which differ only by 1.6% and 0.6% from those refined
against the PXRD data by a Pawley refinement (a =
21.642(1), c = 9.0166(8) Å) (Figure 2a). The systematic
absences could be obtained from the 2D slices cut from the
3D reciprocal lattice (Fig. 1b and Fig. S7) to be 0kl: l = 2n+1;
00l: l = 2n+1, which led to three possible space groups:
P42cm (No. 101), P-4c2 (No. 116), P42/mcm (No. 132).
Ab initio structure solution was performed with each of the three
space groups by direct methods using SIR-2014[30] and atomic
scattering factors for electrons.[31] The space group P-4c2 gave
significantly lower initial R1 value (0.213) than the other two
(0.277 for P42cm and 0.397 for P42/mcm). Thus the initial
structural model with the space group P-4c2 was chosen for the
subsequent structure refinement. The same space was also
suggested by SHELXT. All the metal Co and Ni ions and the linker
Ni-H4TPPP4- positions could be directly located from the initial
structure solution. One solvent DABCO and two H2O molecules
could also be located in the pores from the difference Fourier map.
Table 1. Crystallographic data and structure refinement details of Co-CAU-36.
Sample
Co-CAU-36
Chemical Formula
Data Collection Temperature /K
Wavelength /Å
Space Group
[Co2(Ni-H4TPPP)]·2DABCO·6H2O
96
0,0251
P-4c2
Lattice Parameters /Å
Resolution /Å
a=b=21.980(5), c=8.960(2)
0.83
Completeness /%
Rint
96.7
0.2269
R1, wR2, GoF for F2 > 2 (F2)
σ
0.1356, 0.3364, 1.045
4008 (1978)
192 (81)
Figure 1. (a) SEM image for Co-CAU-36. The crystals are generally rod-like;
the diameters of the rods are usually less than 1 μm. (b) Reconstructed 3D
reciprocal lattice of Co-CAU-36 from cRED data processed using the REDp
software[19]. Inset shows the corresponding crystal (ca 480 nm in size) from
which the cRED data was collected. Some extra diffraction spots from the
nearby tiny crystal were also observed, and excluded in the unit cell
determination and indexing steps.
# Reflections (observed)
# Parameters (restraints)
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Figure 3. (a) PXRD pattern (Cu Kα1, λ = 1.5406 Å) of Co-CAU-36 together with the Pawley fitting profile. (b-c) The framework structure of Co-CAU-36
viewed along (b) [001] and [010] (c). The inorganic building units consist of corner-sharing CoO4 and PO3C tetrahedra and forms 1D chains along [001].
(d) The hydrogen bonding networks between the DABCO molecules and the framework, between the water molecules and the framework as well as
between the water molecules in Co-CAU-36, represented as dashed red lines.
The PXRD pattern simulated from the structural model agrees
well with the experimental one (Figure S9). Because of the
continuous change of the peak positions and significant loss of
the crystallinity upon the removal of the guest species (Figures
S11-13), Rietveld refinement against PXRD data could not be
conducted. Therefore, we carried out independent structure
refinements against each of the eight individual datasets in order
to verify the structural model. The structure refinements
converged to R1 values of 0.136-0.189 for reflections with F2 >
2σ(F2) and 0.164-0.241 for all reflections (Table S1). The atomic
positions refined against the different datasets were compared to
the corresponding positions averaged from the eight models. For
the non-H atoms, the mean deviation is 0.03(2) Å for the
framework atoms (maximum deviation 0.083 Å), 0.10(6) Å for the
DABCO molecule and 0.16(12) Å for the water molecules (Table
S2). The small deviations in the positions of the framework atoms
from the different cRED datasets confirm that the structural
models obtained from each of the single datasets are all correct,
despite the relatively high R1 values compared to those in X-ray
diffraction (see Table S1). We have for the first time been able to
locate and refine the solvent molecules in the pores using cRED
data. The somehow larger deviations in the positions of DABCO
and water molecules are due to their higher mobility inside the
pores compared to the framework atoms constrained by the 3D
coordination network. Figure S11 shows a superposition of the
eight refined structures, where the framework atoms almost
perfectly overlap. We also investigated the effects of data merging
on the final structural model, by comparing the refined structural
model using the cRED data merged from four datasets with those
refined against the four individual datasets. Compared to the
averaged positions from the four individual models, the atomic
positions from the merged data deviate by 0.022(7) Å for the
framework atoms, 0.078(14) Å for DABCO and 0.14(2) Å for water
(Table S3). The crystallographic information files (CIFs) are
deposited in the Cambridge Structure Database, with the CCDC
numbers 1865990 to 1865999.
Thermogravimetric analysis (TGA) and variable temperature
(VT)-PXRD show that Co-CAU-36 is stable above 350 °C upon
the removal of solvent molecules (Figures S11-12), although the
crystallinity decreased significantly. The higher solvent content
given by TGA (Section 5 and Figure S11) compared to that from
the structure refinement can be due to the presence of disordered
solvent molecules. N2 sorption isotherm (Figure 3) shows that Co-
CAU-36 is porous with a BET specific surface area of 700 m2 g-1
and a micropore volume of Vm = 0.3 cm3 g-1. FT-IR spectroscopy
shows a N-H vibration band at 3670 cm-1, indicating the presence
of H-DABCO species, which suggests that the proton is located
at the DABCO molecule instead of at the phosphonate group
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(Figure S14, Table S4). This agrees with the structural model in
which one N in the DABCO acts as an H-donor to form an H-bond
with a bridging framework oxygen (O3). UV/Vis spectroscopy
confirms that Ni is coordinated to the porphyrins (Figure S14 and
S15).
through the Berzilii Center EXSELENT on Porous Materials, and
the Knut and Alice Wallenberg Foundation (KAW) for financial
supports. AKI is supported by the Swedish Foundation for
Strategic Research (SSF) and also a scholarship from KAW.
Keywords: cobalt phosphonate • metal-organic framework •
electron diffraction • structure determination • structure
refinement
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Figure 4. N2-sorption isotherm of Co-CAU-36 measured at 77 K. A specific
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[13]
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In
conclusion,
a
new
and
porous
cobalt
tetraphosphonophenylporphyrin
metal-organic
framework
[Co2(Ni-H4TPPP)]·2DABCO·6H2O, denoted Co-CAU-36, was
synthesized. The crystal structure was determined using the
cRED data collected at low temperature (96 K). Co-CAU-36 is
built from 1D inorganic chains of alternating CoO4 and PO3C
tetrahedra, which form a 3D framework with 1D channels. We
show that not only the framework atoms, but also solvent
molecules in the pores, could be located and refined. Accurate
structural models can be obtained from each of the eight datasets
collected from different crystals. The atomic positions deviated by
less than 0.03(2) Å for the framework atoms, 0.10(6) Å for DABCO
and 0.16(12) Å for water molecules. Hydrogen bonds were
observed between the DABCO and framework, as well as
between the water molecules. The entire structure determination
process, from TEM sample preparation, data collection and
processing, to the final structure solution and refinement, was
conducted within 9 hours. This shows that electron diffraction is
becoming as feasible as X-ray diffraction, and can be used as a
stand-alone method for determination of unknown crystal
structures, from crystals more than 1000 times smaller than those
required even on a synchrotron source.
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The authors thank the Swedish Research Council (VR), Swedish
Governmental Agency for Innovation Systems (VINNOVA)
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Entry for the Table of Contents
COMMUNICATION
Bin Wang, Timo Rhauderwiek, A. Ken
Inge, Hongyi Xu, Taimin Yang, Zhehao
Huang, Norbert Stock*, Xiaodong Zou*
Page No. – Page No.
A porous cobalt tetraphosphonate
metal-organic framework: accurate
structure and guest molecule location
determined by continuous rotation
electron diffraction
Continuous rotation electron diffraction (cRED) was used as a stand-alone method
for both structure solution and refinement of submicron-sized crystals of a novel
cobalt metal-organic framework. We show that the method is robust; not only the
framework structure, but also solvent molecules in the pores could be precisely
located.
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