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  • 1.
    Almqvist, Jonas
    et al.
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Huang, Yafei
    Laaksonen, A
    Wang, Da-Neng
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Docking and homology modeling explain inhibition of the human vesicular glutamate transporters2007In: Protein Science, ISSN 0961-8368, E-ISSN 1469-896X, Vol. 16, no 9, p. 1819-1829Article in journal (Refereed)
    Abstract [en]

    As membrane transporter proteins, VGLUT1-3 mediate the uptake of glutamate into synaptic vesicles at presynaptic nerve terminals of excitatory neural cells. This function is crucial for exocytosis and the role of glutamate as the major excitatory neurotransmitter in the central nervous system. The three transporters, sharing 76% amino acid sequence identity in humans, are highly homologous but differ in regional expression in the brain. Although little is known regarding their three- dimensional structures, hydropathy analysis on these proteins predicts 12 transmembrane segments connected by loops, a topology similar to other members in the major facilitator superfamily, where VGLUT1-3 have been phylogenetically classified. In this work, we present a three- dimensional model for the human VGLUT1 protein based on its distant bacterial homolog in the same superfamily, the glycerol- 3-phosphate transporter from Escherichia coli. This structural model, stable during molecular dynamics simulations in phospholipid bilayers solvated by water, reveals amino acid residues that face its pore and are likely to affect substrate translocation. Docking of VGLUT1 substrates to this pore localizes two different binding sites, to which inhibitors also bind with an overall trend in binding affinity that is in agreement with previously published experimental data.

  • 2. Capitani, GC
    et al.
    Oleynikov, P
    Hovmöller, S
    Stockholm University.
    Mellini, M
    A practical method to detect and correct for lens distortion in the TEM2006In: Ultramicroscopy, Vol. 106, p. 66-74Article in journal (Refereed)
  • 3. Corma, Averlino
    et al.
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Jansson, Kjell
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Sun, Junliang
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Zhang, Daliang
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Jordá, José L.
    Díaz Cabañas, María J.
    Cantín, Ángel
    Moliner, Manuel
    Synthesis and structure of polymorph B of zeolite Beta2008In: Chemistry of Materials, ISSN 0897-4756, E-ISSN 1520-5002, Vol. 20, no 9, p. 3218-3223Article in journal (Refereed)
    Abstract [en]

    It was found that either polymorph B or polymorph C of zeolite beta can be obtained from the same structure directing agent: 4,4-dimethyl-4-azonia-tricyclo[5.2.2.02,6]undec-8-ene hydroxide. The synthesis occurs through a consecutive process where polymorph B is first formed and then transformed into polymorph C. It is possible to produce a zeolite highly enriched in polymorph B, provided that the transformation of this phase into polymorph C is slowed down up to the point where polymorph C is only detected at trace levels. The structure of polymorph B was determined for the first time by electron crystallography with SAED and HRTEM from areas of unfaulted polymorph B crystals.

  • 4. Gemmi, Mauro
    et al.
    Mugnaioli, Enrico
    Gorelik, Tatiana E.
    Kolb, Ute
    Palatinus, Lukas
    Boullay, Philippe
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Abrahams, Jan Pieter
    3D Electron Diffraction: The Nanocrystallography Revolution2019In: ACS central science, ISSN 2374-7943, Vol. 5, no 8, p. 1315-1329Article in journal (Refereed)
    Abstract [en]

    Crystallography of nanocrystalline materials has witnessed a true revolution in the past 10 years, thanks to the introduction of protocols for 3D acquisition and analysis of electron diffraction data. This method provides single-crystal data of structure solution and refinement quality, allowing the atomic structure determination of those materials that remained hitherto unknown because of their limited crystallinity. Several experimental protocols exist, which share the common idea of sampling a sequence of diffraction patterns while the crystal is tilted around a noncrystallographic axis, namely, the goniometer axis of the transmission electron microscope sample stage. This Outlook reviews most important 3D electron diffraction applications for different kinds of samples and problematics, related with both materials and life sciences. Structure refinement including dynamical scattering is also briefly discussed.

  • 5. Grushko, B.
    et al.
    Kapush, D.
    Su, Jie
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Wan, Wei
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Al-rich region of Al-Pt2013In: Journal of Alloys and Compounds, ISSN 0925-8388, E-ISSN 1873-4669, Vol. 580, p. 618-625Article in journal (Refereed)
    Abstract [en]

    The constitution of the Al-rich part of the Al-Pt alloy system is revised. Apart from the previously reported equilibrium Al4Pt, Al21Pt8 and Al2Pt phases, a complex intermetallic was revealed at 7576 at.% Al between 801 and 915 degrees C. Its structure determined by electron diffraction is orthorhombic (Bmmb, a = 1.983, b = 1.636 and c = 1.422 nm).

  • 6.
    Hovmöller, Sven
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zou, Linus Hovmöller
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Grushko, Benjamin
    Structures of pseudo-decagonal approximants in Al-Co-Ni2012In: Philosophical Transactions. Series A: Mathematical, physical, and engineering science, ISSN 1364-503X, E-ISSN 1471-2962, Vol. 370, no 1969, p. 2949-2959Article in journal (Refereed)
    Abstract [en]

    Quasi-crystals shocked the crystallographic world when they were reported in 1984. We now know that they are not a rare exception, and can be found in many alloy systems. One of the richer systems for quasi-crystals and their approximants is Al-Co-Ni. A large series of pseudo-decagonal (PD) approximants have been found. Only two of them, PD4 and PD8, have been solved by X-ray crystallography. We report here the structures of PD1, PD2, PD3 and PD5, solved from the limited information that is provided by electron diffraction patterns, unit cell dimensions and high-resolution electron microscopy images.

  • 7.
    Hovmöller, Sven
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zou, Xiaodong
    Introduction to electron crystallography2011In: Crystal research and technology (1981), ISSN 0232-1300, E-ISSN 1521-4079, Vol. 46, no 6, p. 535-541Article in journal (Refereed)
    Abstract [en]

    Everything in Nature, macroscopic or microscopic, inorganic, organic or biological, has its specific properties. Most properties of matter depend on the atomic structures, and many techniques have been developed over the centuries for structure analysis. The greatest of them all, structure analysis of single crystals by X-ray diffraction, X-ray crystallography, was founded in 1912, and remains the most important technique for studying structures of periodically ordered objects at atomic resolution. Electron diffraction of single crystals was discovered fifteen years later by Thomson, Davisson and Germer. The wave property of electrons was exploited in the invention of the electron microscope by Knoll and Ruska in 1932. Since then, electron microscopes have been used in many fields as a tool for exploring and visualising the microscopic world in all its beauty. Between the first blurred images and today's sharp atomic resolution lies seventy years of untiring engineering. More recently, the unprecedented power of computers has made it possible to analyse quantitatively, and even further improve, these images. The amalgamation of electron diffraction and atomic resolution electron microscopy with crystallographic image processing has created a new powerful tool for structure analysis - electron crystallography.

  • 8. Law, Christopher J.
    et al.
    Almqvist, Jonas
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Bernstein, Adam
    Goetz, Regina M.
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Huang, Yafei
    Soudant, Celine
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Wang, Da-Neng
    Salt-bridge dynamics control substrate-induced conformational change in the membrane transporter GlpT2008In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 378, no 4, p. 828-839Article in journal (Refereed)
    Abstract [en]

    Active transport of substrates across cytoplasmic membranes is of great physiological, medical and pharmaceutical importance. The glycerol-3-phosphate (G3P) transporter (GlpT) of the E. coli inner membrane is a secondary active antiporter from the ubiquitous major facilitator superfamily that couples the import of G3P to the efflux of inorganic phosphate (Pi) down its concentration gradient. Integrating information from a novel combination of structural, molecular dynamics simulations and biochemical studies, we identify the residues involved directly in binding of substrate to the inward-facing conformation of GlpT, thus defining the structural basis for the substrate-specificity of this transporter. The substrate binding mechanism involves protonation of a histidine residue at the binding site. Furthermore, our data suggest that the formation and breaking of inter- and intradomain salt bridges control the conformational change of the transporter that accompanies substrate translocation across the membrane. The mechanism we propose may be a paradigm for organophosphate:phosphate antiporters.

  • 9.
    Li, Mingrun
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Sun, Junliang
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Oleynikov, Peter
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Grushko, Benjamin
    Institut für Festkörperforschung, Forschungszentrum Jülich.
    A complicated quasicrystal approximant ε16 predicted by the strong-reflections approach2010In: Acta Crystallographica Section B: Structural Science, ISSN 0108-7681, E-ISSN 1600-5740, Vol. 66, no part 1, p. 17-26Article in journal (Refereed)
    Abstract [en]

    The structure of a complicated quasicrystal approximant ϵ16 was predicted from a known and related quasicrystal approximant ϵ6 by the strong-reflections approach. Electron-diffraction studies show that in reciprocal space, the positions of the strongest reflections and their intensity distributions are similar for both approximants. By applying the strong-reflections approach, the structure factors of ϵ16 were deduced from those of the known ϵ6 structure. Owing to the different space groups of the two structures, a shift of the phase origin had to be applied in order to obtain the phases of ϵ16. An electron-density map of ϵ16 was calculated by inverse Fourier transformation of the structure factors of the 256 strongest reflections. Similar to that of ϵ6, the predicted structure of ϵ16 contains eight layers in each unit cell, stacked along the b axis. Along the b axis, ϵ16 is built by banana-shaped tiles and pentagonal tiles; this structure is confirmed by high-resolution transmission electron microscopy (HRTEM). The simulated precession electron-diffraction (PED) patterns from the structure model are in good agreement with the experimental ones. ϵ16 with 153 unique atoms in the unit cell is the most complicated approximant structure ever solved or predicted.

  • 10. Oleynikov, P
    et al.
    Demchenko, L
    Christensen, J
    Stockholm University.
    Hovmöller, S
    Stockholm University.
    Yokosawa, T
    Stockholm University.
    Doblinger, M
    Grushko, B
    Zou, XD
    Structure of the pseudodecagonal Al-Co-Ni approximant PD42006In: Philosophical Magazine, Vol. 86, p. 457-462Article in journal (Refereed)
  • 11.
    Oleynikov, Peter
    et al.
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Demchenko, L.
    Christensen, J.
    Hovmöller, Sven Erik
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Yokosawa, T.
    Döblinger, M.
    Grushko, B.
    Zou, X.D.
    Structure of the pseudodecagonal Al–Co–Ni approximant PD42006In: Philosophical Magazine, ISSN 1478-6435, E-ISSN 1478-6443, Vol. 86, no 3-5, p. 457-462Article in journal (Refereed)
    Abstract [en]

    A model for the pseudodecagonal approximant PD4 in the Al–Co–Ni system was deduced from single crystal X-ray diffraction data. The space group is Bbmm with a ?=?101.3, b ?=?32.1 and c ?=?4.1?Å. Atomic positions of 133 unique atoms in the unit cell with a reasonable geometry were found by direct methods and the difference Fourier syntheses. The obtained structure model is in good agreement with high-resolution electron microscopy images of PD4. Diffuse scattering observed along the a * direction in the hkl layers with l ?=?1/2, 3/2 etc. indicates a superstructure with a doubling of the periodicity along the c -axis and a lamellar disorder along the a -axis. If this diffuse scattering is taken into account, c ?=?8.2?Å.

  • 12.
    Oleynikov, Peter
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Gruner, Daniel
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zhang, Daliang
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Sun, Junliang
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Quantitative electron diffraction for crystal structure determination2009In: Electron crystallography for materials research and quantitative characterization of nanostructured materials / [ed] P. Moeck, S.Hovmoeller, S. Nicolopoulos, S.rouvimov, V.Petkov,M.Gateshki, P.Fraundorf, 2009, p. GG01-04Conference paper (Refereed)
    Abstract [en]

    We present a quantitative investigation of data quality using electron precession, compared to standard selected-area electron diffraction (SAED). Data can be collected on a CCD camera and automatically extracted by computer. The critical question of data quality is addressed – can electron diffraction data compete with X-ray diffraction data in terms of resolution, completeness and quality of intensities?

     

     

  • 13.
    Shu, Nanjiang
    et al.
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Zhou, Tuping
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Describing and Comparing Protein Structures Using Shape Strings2008In: Current protein and peptide science, ISSN 1389-2037, E-ISSN 1875-5550, Vol. 9, no 4, p. 310-324Article in journal (Refereed)
    Abstract [en]

    Different methods for describing and comparing the structures of the tens of thousands of proteins that have been determined by X-ray crystallography are reviewed. Such comparisons are important for understanding the structures and functions of proteins and facilitating structure prediction, as well as assessing structure prediction methods. We summarize methods in this field emphasizing ways of representing protein structures as one-dimensional geometrical strings. Such strings are based on the shape symbols of clustered regions of φ/Ψ dihedral angle pairs of the polypeptide backbones as described by the Ramachandran plot. These one-dimensional expressions are as compact as secondary structure description but contain more information in loop regions. They can be used for fast searching for similar structures in databases and for comparing similarities between proteins and between the predicted and native structures.

  • 14.
    Shu, Nanjiang
    et al.
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry, Structural Chemistry.
    Zhou, Tuping
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Prediction of zinc-binding sites in proteins from sequence2008In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 24, no 6, p. 775-782Article in journal (Refereed)
    Abstract [en]

    MOTIVATION: Motivated by the abundance, importance and unique functionality of zinc, both biologically and physiologically, we have developed an improved method for the prediction of zinc-binding sites in proteins from their amino acid sequences. RESULTS: By combining support vector machine (SVM) and homology-based predictions, our method predicts zinc-binding Cys, His, Asp and Glu with 75% precision (86% for Cys and His only) at 50% recall according to a 5-fold cross-validation on a non-redundant set of protein chains from the Protein Data Bank (PDB) (2727 chains, 235 of which bind zinc). Consequently, our method predicts zinc-binding Cys and His with 10% higher precision at different recall levels compared to a recently published method when tested on the same dataset. AVAILABILITY: The program is available for download at www.fos.su.se/~nanjiang/zincpred/download/

  • 15.
    Singh, Devinder
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Panjab University, India.
    Yun, Yifeng
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Wan, Wei
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Grushko, Benjamin
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmoller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Structure determination of a pseudo-decagonal quasicrystal approximant by the strong-reflections approach and rotation electron diffraction2016In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, p. 433-441Article in journal (Refereed)
    Abstract [en]

    The structure of a complicated pseudo-decagonal (PD) quasicrystal approximant in the Al-Co-Ni alloy system, denoted as PD1, was solved by the strong-reflections approach on three-dimensional rotation electron diffraction (RED) data, using the phases from the known PD2 structure. RED shows that the PD1 crystal is primitive and orthorhombic, with a = 37.3, b = 38.8, c = 8.2 angstrom. However, as with other approximants in the PD series, the superstructure reflections (corresponding to c = 8.2 angstrom) are much weaker than those of the main reflections (corresponding to c = 4.1 angstrom), so it was decided to solve the PD1 structure in the smaller primitive unit cell first, i.e. with unit-cell parameters a = 37.3, b = 38.8, c = 4.1 angstrom and space group Pnam. A density map of PD1 was calculated from only the 15 strongest unique reflections. It contained all 31 Co/Ni atoms and many weaker peaks corresponding to Al atoms. The structure obtained from the strong-reflections approach was confirmed by applying direct methods to the complete RED data set. Successive refinement using the RED data set resulted in 108 unique atoms (31 Co/Ni and 77 Al). This is one of the most complicated approximant structures ever solved by electron diffraction. As with other approximants in the PD series, PD1 is built of characteristic 2 nm wheel clusters with fivefold rotational symmetry, which agrees with results from high-resolution electron microscopy images. The simulated electron diffraction patterns for the structure model are in good agreement with the experimental electron diffraction patterns obtained by RED.

  • 16.
    Singh, Devinder
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Yun, Yifeng
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Wan, Wei
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Grushko, Benjamin
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    A complex pseudo-decagonal quasicrystal approximant, Al-37(Co,Ni)(15.5), solved by rotation electron diffraction2014In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 47, no 1, p. 215-221Article in journal (Refereed)
    Abstract [en]

    Electron diffraction is a complementary technique to single-crystal X-ray diffraction and powder X-ray diffraction for structure solution of unknown crystals. Crystals too small to be studied by single-crystal X-ray diffraction or too complex to be solved by powder X-ray diffraction can be studied by electron diffraction. The main drawbacks of electron diffraction have been the difficulties in collecting complete three-dimensional electron diffraction data by conventional electron diffraction methods and the very time-consuming data collection. In addition, the intensities of electron diffraction suffer from dynamical scattering. Recently, a new electron diffraction method, rotation electron diffraction (RED), was developed, which can overcome the drawbacks and reduce dynamical effects. A complete three-dimensional electron diffraction data set can be collected from a sub-micrometre-sized single crystal in less than 2 h. Here the RED method is applied for ab initio structure determination of an unknown complex intermetallic phase, the pseudo-decagonal (PD) quasicrystal approximant Al-37.0(Co,Ni)(15.5), denoted as PD2. RED shows that the crystal is F-centered, with a = 46.4, b = 64.6, c = 8.2 angstrom. However, as with other approximants in the PD series, the reflections with odd l indices are much weaker than those with l even, so it was decided to first solve the PD2 structure in the smaller, primitive unit cell. The basic structure of PD2 with unit-cell parameters a = 23.2, b = 32.3, c = 4.1 angstrom and space group Pnmm has been solved in the present study. The structure with c = 8.2 angstrom will be taken up in the near future. The basic structure contains 55 unique atoms (17 Co/Ni and 38 Al) and is one of the most complex structures solved by electron diffraction. PD2 is built of characteristic 2 nm wheel clusters with fivefold rotational symmetry, which agrees with results from high-resolution electron microscopy images. Simulated electron diffraction patterns for the structure model are in good agreement with the experimental electron diffraction patterns obtained by RED.

  • 17.
    Su, Jie
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Kapaca, Elina
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Liu, Leifeng
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Georgieva, Veselina
    Wan, Wei
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Sun, Junliang
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Valtchev, Valentin
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Structure analysis of zeolites by rotation electron diffraction (RED)2014In: Microporous and Mesoporous Materials, ISSN 1387-1811, E-ISSN 1873-3093, Vol. 189, p. 115-125Article in journal (Refereed)
    Abstract [en]

    Single crystal X-ray diffraction and powder X-ray diffraction (PXRD) are powerful methods for determination of unknown crystal structures including zeolites. However, these techniques have some limitations. For instance, single crystal X-ray diffraction requires large enough crystals which are often difficult to synthesize. For powder X-ray diffraction, peak indexing and intensity extraction become difficult if there exist peak broadening caused by small crystal sizes and peak overlap due to large unit cell and high symmetry. This becomes even more complicated for samples that contain more than one phase. We developed a new rotation electron diffraction (RED) method that can overcome these limitations. Almost complete three-dimensional electron diffraction datasets can be collected from micron- or nano-sized single crystals in a transmission electron microscope by combining electron beam tilt and goniometer tilt. Here, we demonstrate the power and limitations of the RED method for ab initio structure determination of four sub-micron sized zeolites, including a calcined silicalite-1, an EUO-type germanosilicate, an FER-type aluminogermanosilicate and an AST-type aluminogermanosilicate. The latter three zeolites were found in multiphasic samples. We show how the tilt range, tilt step and resolution affect the unit cell determination, structure solution and structure refinement. The EUO-, FER- and AST-type zeolites were found in two multiphasic samples in the Al-Ge-Si system, which were also characterized by PXRD and N-2 sorption.

  • 18.
    Sun, Junliang
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    He, Zhanbing
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Gramm, Fabian
    Baerlocher, Christian
    McCusker, Lynne B.
    Structure determination of the zeolite IM-5 using electron crystallography2010In: Zeitschrift fur Kristallographie, ISSN 0044-2968, Vol. 225, no 03-feb, p. 77-85Article in journal (Refereed)
    Abstract [en]

    The structure of the complex zeolite IM-5 (Cmcm, a = 14.33(4) angstrom. b = 56.9(2) angstrom, c = 20.32(7) angstrom) was determined by combining selected area electron diffraction (SAED), 3D reconstruction of high resolution transmission electron microscopy (HRTEM) images from different zone axes and distance least squares (DLS) refinement. The unit cell parameters were determined from SAED. The space group was determined from extinctions in the SAED patterns and projection symmetries of HRTEM images. Using the structure factor amplitudes and phases of 144 independent reflections obtained from HRTEM images along the [100], [010] and [001] directions, a 3D electrostatic potential map was calculated by inverse Fourier transformation. From this 3D potential map, all 24 unique Si positions could be determined. Oxygen atoms were added between each Si-Si pair and further refined together with the Si positions by distance-least-squares. The final structure model deviates on average 0.16 angstrom for Si and 0.31 angstrom for O from the structure refined using X-ray powder diffraction data. This method is general and offers a new possibility for determining the structures of zeolites and other materials with complex structures.

  • 19.
    Sun, Junliang
    et al.
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Zhang, Daliang
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    He, Zhanbing
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Gramm, Fabian
    Baerlocher, Christian
    McCusker, Lynne B.
    Structure determination of zeolites by electron crystallography2008In: EMC 2008 14th European Microscopy Congress 1–5 September 2008, Aachen, Germany: 1, Instrumentation and methods / [ed] Martina Luysberg, Karsten Tillmann and Thomas Weirich, Berlin Heidelberg: Springer , 2008, p. 757-758Conference paper (Refereed)
    Abstract [en]

    Many zeolite structures have remained unsolved for a long time because of their structural complexity, the size of the crystallites or the presence of defects or impurities. By combining electron microscopy and X-ray powder diffraction data, some of them have been solved (e.g. the high-silica zeolite IM-5, which was first reported in 1998 [1] and recently solved using a charge-flipping structure solution algorithm [2] ), while for other zeolites, good X-ray powder diffraction data are hard to obtain (e.g. polymorph A or B of zeolite Beta). Here we demonstrate a complete structure determination of IM-5 (one of the most complicated zeolited) and polymorph B of zeolite Beta [3] using electron crystallography alone. This shows the power and advantage of structure determination by electron microscopy compared with the X-ray diffraction techniques. The method is general and can be applied to both zeolites and other materials, where the crystals are too small or the structure too complicated to be solved from X-ray powder diffraction data alone [4] . It is particularly useful for structures containing defects.

  • 20.
    Sun, Junliang
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Structure models of quasicrystal approximants deduced from the strong reflections approach in quasicrystals: types, systems and techniques2010In: Quasicrystals: Types, Systems, and Techniques / [ed] Beth E. Puckermann, Nova Science Publishers , 2010Chapter in book (Other academic)
    Abstract [en]

    Quasicrystals are metallic alloys that exhibit atomic scale order, but not periodic order. Atomic scale properties of these materials are different from single crystalline material, for example, extraordinary mechanical properties, electrical and thermal transport properties, and electronic structure. This book presents topical research in the study of quasicrystals, including vacancies in quasicrystals; the formation of quasicrystals in bulk metallic glasses and their effects on mechanical behavior; the electrical transport observed in Al-Pd-Mn quasicrystals; logarithmic periodicity in quasicrystals; and positron annihilation studies of quasicrystals.

     

  • 21.
    Todde, Guido
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab). Wallenberg Research Centre at Stellenbosch University, South Africa.
    Influence of Antifreeze Protein on the Ice/Water Interface2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 8, p. 3407-3413Article in journal (Refereed)
    Abstract [en]

    Antifreeze proteins (AFP) are responsible for the survival of several species, ranging from bacteria to fish, that encounter subzero temperatures in their living environment. AFPs have been divided into two main families, moderately and hyperactive, depending on their thermal hysteresis activity. We have studied one protein from both families, the AFP from the snow flea (sfAFP) and from the winter flounder (wfAFP), which belong to the hyperactive and moderately active family, respectively. On the basis of molecular dynamics simulations, we have estimated the thickness of the water/ice interface for systems both with and without the AFPs attached onto the ice surface. The calculation of the diffusion profiles along the simulation box allowed us to measure the interface width for different ice planes. The obtained widths clearly show a different influence of the two AFPs on the ice/water interface. The different impact of the AFPs here studied on the interface thickness can be related to two AFPs properties: the protein hydrophobic surface and the number of hydrogen bonds that the two AFPs faces form with water molecules.

  • 22.
    Todde, Guido
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab).
    Influence of mutations at the proximal histidine position on the Fe-O-2 bond in hemoglobin from density functional theory2016In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 144, no 9, article id 095101Article in journal (Refereed)
    Abstract [en]

    Four mutated hemoglobin (Hb) variants and wild type hemoglobin as a reference have been investigated using density functional theory methods focusing on oxygen binding. Dispersion-corrected B3LYP functional is used and found to provide reliable oxygen binding energies. It also correctly reproduces the spin distribution of both bound and free heme groups as well as provides correct geometries at their close vicinity. Mutations in hemoglobin are not only an intrigued biological problem and it is also highly important to understand their effects from a clinical point of view. This study clearly shows how even small structural differences close to the heme group can have a significant effect in reducing the oxygen binding of mutated hemoglobins and consequently affecting the health condition of the patient suffering from the mutations. All of the studied mutated Hb variants did exhibit much weaker binding of molecular oxygen compared to the wild type of hemoglobin.

  • 23.
    Todde, Guido
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    The Influence of Mutations at the Proximal Histidine Position on the Fe-O2 Bond in Hemoglobin from Density Functional TheoryManuscript (preprint) (Other academic)
  • 24.
    Todde, Guido
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). University of Cagliari, Italy; Stellenbosch University, South Africa.
    Mocci, Francesca
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). University of Cagliari, Italy.
    Glucose oxidase from Penicillium amagasakiense: Characterization of the transition state of its denaturation from molecular dynamics simulations2014In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 82, no 10, p. 2353-2363Article in journal (Refereed)
    Abstract [en]

    Glucose oxidase (GOx) is a flavoenzyme having applications in food and medical industries. However, GOx, as many other enzymes when extracted from the cells, has relatively short operational lifetimes. Several recent studies (both experimental and theoretical), carried out on small proteins (or small fractions of large proteins), show that a detailed knowledge of how the breakdown process starts and proceeds on molecular level could be of significant help to artificially improve the stability of fragile proteins. We have performed extended molecular dynamics (MD) simulations to study the denaturation of GOx (a protein dimer containing nearly 1200 amino acids) to identify weak points in its structure and in this way gather information to later make it more stable, for example, by mutations. A denaturation of a protein can be simulated by increasing the temperature far above physiological temperature. We have performed a series of MD simulations at different temperatures (300, 400, 500, and 600 K). The exit from the protein's native state has been successfully identified with the clustering method and supported by other methods used to analyze the simulation data. A common set of amino acids is regularly found to initiate the denaturation, suggesting a moiety where the enzyme could be strengthened by a suitable amino acid based modification.

  • 25.
    Todde, Guido
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Whitman, Christopher
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Cittadella Universitaria di Monserrato, Italy.
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab). Stellenbosch University, South Africa.
    Induced Ice Melting by the Snow Flea Antifreeze Protein from Molecular Dynamics Simulations2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 47, p. 13527-13534Article in journal (Refereed)
    Abstract [en]

    Antifreeze proteins (AFP) allow different life forms, insects as well as fish and plants, to survive in subzero environments. AFPs prevent freezing of the physiological fluids. We have studied, through molecular dynamics simulations, the behavior of the small isoform of the AFP found in the snow flea (sfAFP), both in water and at the ice/water interface, of four different ice planes. In water at room temperature, the structure of the sfAFP is found to be slightly unstable. The loop between two polyproline II helices has large fluctuations as well as the C-terminus. Torsional angle analyses show a decrease of the polyproline II helix area in the Ramachandran plots. The protein structure instability, in any case, should not affect its antifreeze activity. At the ice/water interface the sfAFP triggers local melting of the ice surface. Bipyramidal, secondary prism, and prism ice planes melt in the presence of AFP at temperatures below the melting point of ice. Only the basal plane is found to be stable at the same temperatures, indicating an adsorption of the sfAFP on this ice plane as confirmed by experimental evidence.

  • 26.
    Wan, Wei
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Structure projection reconstruction from through focus series of high resolution transmission electron microscopy images2012In: Ultramicroscopy, ISSN 0304-3991, E-ISSN 1879-2723, Vol. 115, p. 50-60Article in journal (Refereed)
    Abstract [en]

    A structure projection reconstruction method based on contrast transfer function correction of through-focus series of high-resolution transmission electron microscopy images is presented. In this method, defocus values are determined by evaluating phase similarities of the pixels on the Fourier transforms of the images after correction using trial defocus values. Two-fold astigmatism is also determined, by measuring focus variation along different directions. Each image in the series is corrected for the effects of contrast transfer function and then combined into a structure projection image. The method works for both crystalline and non-crystalline objects. Test results with experimental images are presented. Influences of experimental parameters for imaging and effects of crystal thickness on reconstruction are discussed.

  • 27.
    Wan, Wei
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Sun, Junliang
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Su, Jie
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Three-dimensional rotation electron diffraction: software RED for automated data collection and data processing2013In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 46, p. 1863-1873Article in journal (Refereed)
    Abstract [en]

    Implementation of a computer program package for automated collection and processing of rotation electron diffraction (RED) data is described. The software package contains two computer programs: RED data collection and RED data processing. The RED data collection program controls the transmission electron microscope and the camera. Electron beam tilts at a fine step (0.05-0.20 degrees) are combined with goniometer tilts at a coarse step (2.0-3.0 degrees) around a common tilt axis, which allows a fine relative tilt to be achieved between the electron beam and the crystal in a large tilt range. An electron diffraction (ED) frame is collected at each combination of beam tilt and goniometer tilt. The RED data processing program processes three-dimensional ED data generated by the RED data collection program or by other approaches. It includes shift correction of the ED frames, peak hunting for diffraction spots in individual ED frames and identification of these diffraction spots as reflections in three dimensions. Unit-cell parameters are determined from the positions of reflections in three-dimensional reciprocal space. All reflections are indexed, and finally a list with hkl indices and intensities is output. The data processing program also includes a visualizer to view and analyse three-dimensional reciprocal lattices reconstructed from the ED frames. Details of the implementation are described. Data collection and data processing with the software RED are demonstrated using a calcined zeolite sample, silicalite-1. The structure of the calcined silicalite-1, with 72 unique atoms, could be solved from the RED data by routine direct methods.

  • 28.
    Wang, Bin
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    A method for determination of angular accuracy of the goniometer on a transmission electron microscopeManuscript (preprint) (Other academic)
    Abstract [en]

    For collection and reconstruction of 3D electron diffraction or electron tomography data, it is essential to have reliable goniometer tilt angles. Thus, it is important to know the accuracy of tilt angles a goniometer can provide on a transmission electron microscope (TEM).  In this paper, a method to determine the angular accuracy of a goniometer is presented, which is based on the orientation determination of rotation electron diffraction (RED) data from a crystal with known unit cell. The method was demonstrated on a JEOL JEM 2100 LaB6 TEM. The result showed that the uncertainty for the goniometer was 1.75% from the expected rotation angle. Meanwhile, the readout error from the TEM hardware followed a combination of sinusoidal and linear components, indicating a more complicated readout error source than only linear errors. A quality assessment method for general TEM goniometers is proposed.

  • 29. Wang, Bin
    et al.
    Wan, Wei
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Waterman, David
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    A method for accurate orientation determination for rotation electron diffraction patternsManuscript (preprint) (Other academic)
    Abstract [en]

    A numerical method for calculating the frame orientation of a crystal from indexed electron diffraction patterns is developed. The algorithm uses the observed reflection indices and unit cell parameters of the crystal, and operates by minimizing the summed distances in reciprocal space between the observed reflections and the Ewald sphere. Partiality correction is proposed by making use of the information about the rotation axis. The accuracy of the orientations is found to be around 0.01° for each of the frames in a rotation dataset.

  • 30.
    Xu, Hongyi
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Lebrette, Hugo
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Yang, Taimin
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Srinivas, Vivek
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Högbom, Martin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    A Rare Lysozyme Crystal Form Solved Using Highly Redundant Multiple Electron Diffraction Datasets from Micron-Sized Crystals2018In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 26, no 4, p. 667-675Article in journal (Refereed)
    Abstract [en]

    Recent developments of novel electron diffraction techniques have shown to be powerful for determination of atomic resolution structures from micronand nano-sized crystals, too small to be studied by single-crystal X-ray diffraction. In this work, the structure of a rare lysozyme polymorph is solved and refined using continuous rotation MicroED data and standard X-ray crystallographic software. Data collection was performed on a standard 200 kV transmission electron microscope (TEM) using a highly sensitive detector with a short readout time. The data collection is fast (similar to 3 min per crystal), allowing multiple datasets to be rapidly collected from a large number of crystals. We show that merging data from 33 crystals significantly improves not only the data completeness, overall I/sigma and the data redundancy, but also the quality of the final atomic model. This is extremely useful for electron beam-sensitive crystals of low symmetry or with a preferred orientation on the TEM grid.

  • 31.
    Yun, Yifeng
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Wan, Wei
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Rabbani, Faiz
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Su, Jie
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Xu, Hongyi
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Johnsson, Mats
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Phase identification and structure determination from multiphase crystalline powder samples by rotation electron diffraction2014In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 47, p. 2048-2054Article in journal (Refereed)
    Abstract [en]

    Phase identification and structure characterization are important in synthetic and materials science. It is difficult to characterize the individual phases from multiphase crystalline powder samples, especially if some of the phases are unknown. This problem can be solved by combining rotation electron diffraction (RED) and powder X-ray diffraction (PXRD). Four phases were identified on the same transmission electron microscopy grid from a multiphase sample in the Ni-Se-O-Cl system, and their structures were solved from the RED data. Phase 1 (NiSeO3) was found in the Inorganic Crystal Structure Database using the information from RED. Phase 2 (Ni3Se4O10Cl2) is an unknown compound, but it is isostructural to Co3Se4O10Cl2, which was recently solved by single-crystal X-ray diffraction. Phase 3 (Ni5Se6O16Cl4H2) and Phase 4 (Ni5Se4O12Cl2) are new compounds. The fact that there are at least four different compounds in the as-synthesized material explains why the phase identification and structure determination could not be done by PXRD alone. The RED method makes phase identification from such multiphase powder samples much easier than would be the case using powder X-ray diffraction. The RED method also makes structure determination of submicrometre-sized crystals from multiphase samples possible.

  • 32.
    Yun, Yifeng
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Wan, Wei
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Rabbani, Faiz
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Su, Jie
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Xu, Hongyi
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Johnsson, Mats
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Phase identification and structure determination from multiphasic crystalline powder samples by rotation electron diffractionIn: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767Article in journal (Refereed)
    Abstract [en]

    Phase identification and structure characterisation are important in synthetic and material science. It is difficult to characterise the individual phases from multiphasic crystalline powder samples, especially if some of the phases are unknown. Here we describe how this problem can be solved by combining rotation electron diffraction (RED) and powder X-ray diffraction (PXRD). Four phases were identified on the same transmission electron microscopy (TEM) grid from a multiphasic sample in the Ni-Se-O-Cl system and their structures were solved from the RED data. Phase 1 (NiSeO3) was found in the Inorganic Crystal Structure Data (ICSD) database using the information from RED. Phase 2 (Ni3Se4O10Cl2) is an unknown compound but it is iso-structural to Co3Se4O10Cl2, which was recently solved by single crystal X-ray diffraction. Phase 3 (Ni5Se6O16Cl4H2) and Phase 4 (Ni5Se4O12Cl2) are new compounds. The fact that there are at least four different compounds in the as-synthesised material explains why the phase identification and structure determination could not be done only by PXRD. The RED method makes phase identification from such multiphasic powder samples much easier compared to powder X-ray diffraction. The RED method also makes structure determination of submicron-sized crystals from multiphasic samples possible.

  • 33.
    Yun, Yifeng
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Wan, Wei
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Three-dimensional electron diffraction as a complementary technique to powder X-ray diffraction for phase identification and structure solution of powders2015In: IUCrJ, ISSN 2052-2525, Vol. 2, p. 267-282Article in journal (Refereed)
    Abstract [en]

    Phase identification and structure determination are important and widely used techniques in chemistry, physics and materials science. Recently, two methods for automated three-dimensional electron diffraction (ED) data collection, namely automated diffraction tomography (ADT) and rotation electron diffraction (RED), have been developed. Compared with X-ray diffraction (XRD) and two-dimensional zonal ED, three-dimensional ED methods have many advantages in identifying phases and determining unknown structures. Almost complete three-dimensional ED data can be collected using the ADT and RED methods. Since each ED pattern is usually measured off the zone axes by three-dimensional ED methods, dynamic effects are much reduced compared with zonal ED patterns. Data collection is easy and fast, and can start at any arbitrary orientation of the crystal, which facilitates automation. Threedimensional ED is a powerful technique for structure identification and structure solution from individual nano-or micron-sized particles, while powder X-ray diffraction (PXRD) provides information from all phases present in a sample. ED suffers from dynamic scattering, while PXRD data are kinematic. Three-dimensional ED methods and PXRD are complementary and their combinations are promising for studying multiphase samples and complicated crystal structures. Here, two three-dimensional ED methods, ADTand RED, are described. Examples are given of combinations of three-dimensional ED methods and PXRD for phase identification and structure determination over a large number of different materials, from Ni-Se-O-Cl crystals, zeolites, germanates, metal-organic frameworks and organic compounds to intermetallics with modulated structures. It is shown that three-dimensional ED is now as feasible as X-ray diffraction for phase identification and structure solution, but still needs further development in order to be as accurate as X-ray diffraction. It is expected that three-dimensional ED methods will become crucially important in the near future.

  • 34.
    Zhang, Daliang
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Grüner, Daniel
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Oleynikov, Peter
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Wan, Wei
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Precession Electron Diffraction Using a Digital Sampling Method2010In: Ultramicroscopy, ISSN 0304-3991, E-ISSN 1879-2723, Vol. 211, no 1, p. 47-55Article in journal (Refereed)
    Abstract [en]

    A software-based method for collecting precession electron diffraction (PED) patterns isdescribed. The PED patterns are obtained on a computer controlled transmission electronmicroscope. A series of electron diffraction (ED) patterns are collected as still ED frames atequal intervals while the electron beam is precessed by one period (360°) around the opticalaxis. A PED pattern is obtained by combining the different ED frames, which resembles thesampling of a conventional PED pattern. Since intermediate ED frames are collected, it ispossible to perform different post-processing strategies on the ED data. This can be used forgeometric corrections to obtain accurate integrated intensities. The alignments and datacollection are fully automated and controlled by software. The data quality is comparable towhat can be achieved using specialized hardware for precession. The PED data can be usedfor structure solution and refinement with reasonably good R-values.

  • 35.
    Zhang, Daliang
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Oleynikov, Peter
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Collecting 3D electron diffraction data by the rotation method2010In: Zeitschrift fur Kristallographie, ISSN 0044-2968, Vol. 225, no 2-3, p. 94-102Article in journal (Refereed)
    Abstract [en]

    A new method for collecting complete three-dimensional electron diffraction data is described. Diffraction data is collected by combining electron beam tilt at many very small steps, with rotation of the crystal in a few but large steps. A number of practical considerations are discussed, as well as advantages and disadvantages compared to other methods of collecting electron diffraction data.

  • 36. Zhang, H
    et al.
    He, ZB
    Oleynikov, P
    Zou, XD
    Hovmöller, S
    Stockholm University.
    Kuo, KH
    Structure model for the tau(mu) phase in Al-Cr-Si alloys deduced from the lambda phase by the strong-reflections approach2006In: Acta Crystallographica Section B-Structural Science, Vol. 62, p. 16-25Article in journal (Refereed)
  • 37. Zhang, H
    et al.
    Zou, XD
    Oleynikov, P
    Hovmöller, S
    Stockholm University.
    Structure relations in real and reciprocal space of hexagonal phases related to i-ZnMgRE quasicrystals2006In: Philosophical Magazine, Vol. 86, p. 543-548Article in journal (Refereed)
  • 38. Zhang, H
    et al.
    Zou, XD
    Oleynikov, P
    Hovmöller, S
    Stockholm University.
    Structure relations in real and reciprocal space of hexagonal phases related to i-ZnMgRE quasicrystals2006In: Philosophical Magazine, Vol. 86, p. 543-548Article in journal (Refereed)
  • 39. Zhang, H.
    et al.
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Oleynikov, Peter
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Hovmöller, Sven Erik
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Structure relations in real and reciprocal space of hexagonal phases related to i-ZnMgRE quasicrystals2006In: Philosophical Magazine, ISSN 1478-6435, E-ISSN 1478-6443, Vol. 86, no 3-5, p. 343-348Article in journal (Refereed)
    Abstract [en]

    The µ 3 , µ 5 and µ 7 approximants in Mg-Zn-RE were related in real and reciprocal space. The structure factors of µ 3 , µ 5 and µ 7 have quite similar intensity distributions and identical phases for the strongest corresponding reflections. Structure models of any of µ 3 , µ 5 and µ 7 can be obtained from any of the others using the strong reflections approach.

  • 40.
    Zhang, Hongqiang
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    He, Z.B.
    Oleynikov, Peter
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Hovmöller, Sven Erik
    Stockholm University, Faculty of Science, Department of Physics.
    Zou, X.D.
    Kuo, K.H.
    A structure model for τ(μ) phase in Al-Cr-Si alloys deduced from λ phase by the strong reflections approach2006In: Acta Crystallographica Section B: Structural Science, ISSN 0108-7681, E-ISSN 1600-5740, Vol. 62, no 1, p. 16-25Article in journal (Refereed)
    Abstract [en]

    There are very obvious common features in the electron diffraction patterns of the λ and τ(μ) phases in the Al–Cr–Si system. The positions of the strong reflections and their intensity distributions are similar for the two structures. The relation of the reciprocal lattices of the λ and τ(μ) phases is studied. By applying the strong-reflections approach, the structure factors of τ(μ) are deduced from the corresponding structure factors of the known λ phase. Rules for selecting reflections for the strong-reflections approach are described. Similar to that of λ, the structure of τ(μ) contains six layers stacked along the c axis in each unit cell. There are 752 atoms in each unit cell, 53 of them are unique. The corresponding composition of the τ(μ) model is Al3.82  −  xCrSix. Simulated electron diffraction patterns from the structure model are in good agreement with the experimental ones. The arrangement of interpenetrated icosahedral clusters in the τ(μ) phase is discussed.

  • 41.
    Zhou, Tuping
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Shu, Nanjiang
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    A Novel Method for Accurate One-dimensional Protein Structure Prediction Based on Fragment Matching2010In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 26, no 4, p. 470-477Article in journal (Refereed)
    Abstract [en]

    Motivation: The precise prediction of one-dimensional (1D) protein structure as represented by the protein secondary structure and 1D string of discrete state of dihedral angles (i.e. Shape Strings) is a prerequisite for the successful prediction of three-dimensional (3D) structure as well as protein-protein interaction. We have developed a novel 1D structure prediction method, called Frag1D, based on a straightforward fragment matching algorithm and demonstrated its success in the prediction of  three sets of 1D structural alphabets, i.e. the classical three-state secondary structure, three-state Shape Strings and eight-state Shape Strings.

    Results: By exploiting the vast protein sequence and protein structure data available, we have brought secondary structure prediction closer to the expected theoretical limit. When tested by a leave-one-out cross validation on a non-redundant set of PDB cutting at 30% sequence identity containing 5860 protein chains, the overall per-residue accuracy for secondary structure prediction, i.e. Q3 is 82.9%. The overall per-residue accuracy for three-state and eight-state Shape Strings are 85.1% and 71.5% respectively. We have also benchmarked our program with the latest version of PSIPRED for secondary structure prediction and our program predicted 0.3% better in Q3 when tested on 2241 chains with the same training set. For Shape Strings, we compared our method with a recently published method with the same dataset and definition as used by that method. Our program predicted at 2.2% better in accuracy for three-state Shape Strings. By quantitatively investigating the effect of data base size on 1D structure prediction we show that the accuracy increases by about 1% with every doubling of the database size.

  • 42.
    Zou, Xiaodong
    et al.
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Wan, Wei
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Quantitative 3D electron microscopy and 3D electron diffraction2010In: Journal of Chinese Electron Microscopy Society, Vol. 29, p. 230-243Article in journal (Refereed)
    Abstract [en]

    Electron crystallography can be used for determination of atomic structures of micrometer-/ nanometer-sized crystals, which are million times smaller than those required by X-ray crystallography. Structure determination at atomic resolution can be done from both high-resolution electron microscopy images combined with crystallographic image processing and electron diffraction data, or by combining them with powder X-ray diffraction data. Atoms may be overlapped in all projections if the unit cell of the crystal is large. In such cases, atomic structures can be obtained by collecting several diffraction patterns and images from different directions and combining them to reconstruct a three-dimensional potential map. In this paper, some recent developments of electron crystallography and its applications in structure determination of inorganic crystals in the past decade are shown.

     

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