General Interest II

Conference: 2020: 70th ACA Annual Meeting
08/06/2020: 12:00 PM  - 3:00 PM 
4.2.3 
Oral Session 
Virtual  

Description

General Interest sessions are the forum for topics of broad interest to the crystallographic community or for presentations that do not fit the specific theme of other sessions. All presentations are selected from submitted abstracts.

Presentations

The Order of the Fullerene

12:00 PM - 12:20 PM 
The high symmetry of empty cage as well as endohedral fullerenes leads to orientational disorder in crystal structures . Often the extent of disorder prevents visibility of clean bonds and accurate measurement of bond lengths. This issue is especially cumbersome when a higher fullerene has a number of possible cage isomers, each of which is identifiable only through high-resolution single crystal data. A solution to the problem can be found in the phenomenon of cocrystallization – harnessing the non-covalent interaction between the fullerene and a second molecule (the cocrystallization agent) for ordering the unwieldy fullerene. In this systematic study, we crystallographically characterize the ordering interaction between C60 (the model fullerene) and late transition metal octaethylporphyrin [MII(OEP)] units (the chosen cocrystallization agents). Minor variations in the cocrystallization setup can dramatically influence the conformation of porphyrin molecules as well as the stoichiometry of their combination with C60. Such factors are examined, and their effects described in this work. 

View Proposal 225

Author

Mrittika Roy, University of California, Davis Davis, CA 

Additional Author(s)

Marilyn Olmstead, Dept of Chemistry, Univ of California Davis
Alan Balch, University of California, Davis Davis, CA 

Can 3D Electron Diffraction Provide Accurate Atomic Structures of Metal-Organic Frameworks?

12:20 PM - 12:40 PM 
Many framework materials such as metal-organic frameworks (MOF) or porous coordination polymers (PCPs) are synthesized as polycrystalline powders, which are too small for structure determination by single crystal X-ray diffraction (SCXRD). Here, we show that a three-dimensional (3D) electron diffraction method, namely continuous rotation electron diffraction (cRED), can be used for ab initio structure determination of such materials. As an example, we present a complete structural analysis of a biocomposite, denoted BSA@ZIF-CO3-1, where Bovin Serum Albumin (BSA) was encapsulated in a zeolitic imidazolate framework (ZIF). Low electron dose was combined with ultrafast cRED data collection to minimize electron beam damage of the sample. We demonstrate that the atomic structure obtained by cRED is as reliable and accurate as that obtained by single crystal X-ray diffraction. The high accuracy and fast data collection open new opportunities for investigation of cooperative phenomena in framework structures at atomic level. 

View Proposal 218

Author

Meng Ge, Stockholm University Stockholm

Additional Author(s)

Zhehao Huang, Stockholm University Stockholm
Xiaodong Zou, Stockholm University Stockholm, Sweden 

When the unusual is the normal: making non-standard structural studies routine.

12:40 PM - 1:00 PM 
We present several problematic small-molecule structures that required non-routine handling of data collection, processing and/or structural refinement. The structure of an octahedral Ni(II) complex could not be properly refined until the crystal was identified as a pseudo-merohedral twin. A highly absorbing complex [C[sub]6[/sub]H[sub]5[/sub]CH[sub]2[/sub]CH[sub]2[/sub]NH[sub]3[/sub]][sub]2[/sub][CH[sub]3[/sub]NH[sub]3[/sub]][Pb[sub]2[/sub]I[sub]7[/sub]] (μMo = 25.54 mm[sup]-1[/sup]) required a careful choice of crystal, radiation source, and subsequent positional disorder modelling. A sample of an organic salt contained non-merohedrally twinned crystals only; upon exploring multiple absorption correction choices with TWINABS, the structural model necessitated use of the Platon SQUEEZE protocol for modeling of disordered solvent electron density. A Co(II) complex required lowering the crystallographic symmetry from space group [i]C[/i]2/[i]c[/i] to [i]C[/i][i]c[/i], identifying solvent of crystallization, and then finally establishing the chemical identity of the metal center. Finally, a chiral [i]P[/i]1 organic salt whose crystals decomposed due to radiation damage during the X-ray measurement required two data collections to achieve a data set that had a sufficient data completeness for the subsequent structural refinement process. 

View Proposal 148

Author

Amelia Wheaton, University of Wisconsin at Madison Department of Chemistry Madison, WI 

Additional Author

Ilia Guzei, Chemistry, UW Madison

Coffee Break

1:00 PM - 1:20 PM 

Partially Ordered Sets in Crystallography

1:20 PM - 1:40 PM 
I have always enjoyed examining crystallography through the lens of abstract algebra. In college, I had a double major of pure mathematics and physics. This work is part of a chapter in my next book. Partially ordered sets are an excellent device to explore the relations among both point groups and space groups. Figure 1 is a Hasse diagram or tree of the three-dimensional point groups [1]. (Unfortunately, the word order has two different meanings. In 'partially ordered sets', order refers to sequence, in the 'order of a point group' order means the number of elements in the point group.) In my talk, set elements and ordering relations are defined. Partially ordered sets have 'incomparable' elements. A totally ordered set is a chain. The two-dimensional point group trees are labeled with the general position and symbol stereographic projection symbols. In my talk, the duality principle is applied to three-dimensional point groups to explore the relationships among the centrosymmetric point groups and piezoelectricity. At the Curie temperature barium titinate goes from a strongly piezoelectric material to a nonpiezoelectric material. Isomorphism is demonstrated in three systems: first, between the three-dimensional monoclinic and orthorhombic crystal systems; second, between the tetragonal and hexagonal systems; and third, between the trigonal and cubic systems. Mappings are given. The cubic system is an example of mathematical lattice. The two-dimensional space group tree has the order of the associated point group plotted along the y-axis. This is necessary because the individual space groups themselves are infinite. In my talk, the seven rectangular space groups are illustrated. The three-dimensional Type I space group Hasse diagram for space group 2, P, is shown limited to its maximal subgroups and minimal supergroups. Finally, Type I trees are shown for the 13 monoclinic space groups. Reference [1] Julian, Maureen M. Foundations of Crystallography with Computer Applications, 2nd edition, CRC Press: New York (2015), ISBN: 978-1466552913. Figure 3.54 p.131. 

View Proposal 282

Author

Maureen Julian, Virginia Tech Blacksburg, VA 

Study on structure, electrical and dielectric properties of pure and Sr-doped LaCoO3 for chemical sensor application.

1:40 PM - 2:00 PM 
A perovskite LaCoO3 was prepared by combustion and citrate-gel methodsin order to test its possible application as a chemical sensor. The crystal evolution, structure, composition, texture, morphology, and particle size were analyzed by X-ray diffraction, BET and scanning electron microscopies. The effects of doped Sr+2 on crystal structure distortion, magnetic, and electrical properties with perovskites structure La1 xSrxCoO3 where (x = 0.2, 0.5, 0.8) have been investigated also. It was found that La+3 is gradually replaced by Sr+2, the changes from monoclinic to high symmetry cubic with the structure La0.2Sr0.8CoO3, resulting in a change in the bond angle as well as the bond length between Co-O. The changes in bond angle and bond length influence both electrical and magnetic properties of the system as expected. Crystal spilt Calculations predict that the bigger size of Sr+2 reducing the splitting energy gap thus improving the electronic conductivity of perovskites. Also, Sr+2 doping converts Co+3 to Co+4 and brings holes in the p-type semiconductor. Thus, increasing the resistance variation range of LaCoO3, enhancing the sensing performance. The temperature variation of the resistivity shows that these compounds have semiconductor behavior. The frequency dependence of the dielectric constant in these materials indicates that space charge polarization contributes significantly to their observed dielectric parameters. Keywords: perovskite LaCoO3, Rare earth, chemical sensors, dielectric properties, electrical resistivity. 

View Proposal 261

Author

Norah Alhaqbani Riyadh

Determining Atomic Structures from Digitally Defined Regions of Nanocrystals

2:00 PM - 2:20 PM 
Crystallography is intrinsically limited by its reliance on signal averaged over large collections of perfectly ordered molecules within a single crystal lattice or even across multiple crystals. This is particularly pronounced when crystals contain severe disorder pathologies or are beam sensitive. Recent advances in x-ray and electron diffraction have reduced the minimum size of crystals useful for structure determination to 100s of nms1–3, overcoming many of these difficulties. We previously applied 4-dimensional scanning transmission electron microscopy (4D-STEM), a scanning diffraction technique, to the study of nanomosaicity within a single micron-scale crystal4. This highlighted a potential opportunity for using scanning nano-beam diffraction for structure determination. In our current work, we extend developments in 4D-STEM by incorporating tomography to solve atomic structures of macromolecules from specific regions of polymer nanocrystals. Scanning nanobeam electron diffraction tomography (nanoEDT) consists of scanning a sub-10nm electron probe over a peptide nanocrystal whilst rotating the crystal in discrete, 1-degree intervals5. At each tilt angle, a 4D-STEM dataset is collected by a direct electron detector, capturing thousands of sparse diffraction patterns mapped to specific locations within the crystal. The use of direct electron detection, in combination with cryogenic data collection and a hybrid counting algorithm, allows even weak signals from high-resolution Bragg peaks to be accurately recorded from radiation-sensitive crystals. This intensity data, representing an angular wedge of reciprocal space, is extracted from computationally defined regions of the scan and used to compute structures via fragment-based phasing methods. By scanning the beam, we can collect diffraction from a wide field-of-view and digitally recombine it for later analysis, obviating the need for a selected area aperture. Data collected by nanoEDT compares favourably with data acquired under more conventional electron diffraction methodologies (microED), with minimal evidence of radiation damage. NanoEDT breaks new ground in nanocrystallography by allowing atomic structures to be determined from any region of a nanocrystal through the use of virtual apertures, potentially leading to the determination of atomic structures from heterogeneous or polycrystalline nanoassemblies. References 1. Lanza, A. et al. Nanobeam precession-assisted 3D electron diffraction reveals a new polymorph of hen egg-white lysozyme. IUCrJ 6, (2019). 2. Mugnaioli, E. et al. Ab Initio Structure Determination of Cu2–x Te Plasmonic Nanocrystals by Precession-Assisted Electron Diffraction Tomography and HAADF-STEM Imaging. Inorganic chemistry 57, 10241–10248 (2018). 3. Sawaya, M. R. et al. Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED. PNAS 113, 11232–11236 (2016). 4. Gallagher-Jones, M. et al. Nanoscale mosaicity revealed in peptide microcrystals by scanning electron nanodiffraction. Communications Biology 2, 26 (2019). 5. Gallagher-Jones, M. et al. Atomic structures determined from digitally defined nanocrystalline regions. IUCrJ 7, 3 (2020) 

View Proposal 303

Author

Marcus Gallagher-Jones, UCLA Los angeles, CA 

Additional Author(s)

Karen Bustillo, Lawrence Berkeley National Laboratory Berkeley, CA 
Colin Ophus, Lawrence Berkeley National Laboratory Berkeley, CA 
Logan Richards, UCLA Los angeles, CA 
Jim Ciston, Lawrence Berkeley National Laboratory Berkeley, CA 
Sangho Lee, Sungkyunkwan University Suwon
Andrew Minor, University of California Berkeley Berkeley, CA 
Jose Rodriguez, UCLA Los angeles, CA 

The ISOTILT program for discovering cooperative rigid-unit modes (RUMs) in crystalline solids

2:20 PM - 2:40 PM 
Structural phase transitions in crystalline materials with networks of interconnected rigid units require that any rigid-unit modes (RUMs) be largely cooperative in nature to avoid distorting the rigid units or pulling them apart. For three-dimensional networks, cooperation can be a rather severe constraint, so that RUMs can be difficult to identify when they exist at all. A new approach to discovering RUMs was recently reported [1], in which linearizing the network constraints in the limit of small rotations transformed a non-linear trigonometric problem into a homogeneous linear system of equations. We now report a series of theoretical advances that has made it possible to identify RUMs quickly and accurately, even in very large and complicated systems. The original method, enhanced by these advances, has now been implemented as a new web-based software program called ISOTILT, and included as part of the ISOTROPY Software Suite. [2] [1] B. J. Campbell, C. J. Howard, T. B. Averett, T. A. Whittle, S. Schmid, S. Machlus, C. Yost, H. T. Stokes, Acta Cryst. A 74, 408-424 (2018). [2] H. T. Stokes, D. M. Hatch, B. J. Campbell, ISOTROPY Software Suite, iso.byu.edu. 

View Proposal 352

Author

Branton Campbell, Brigham Young University Springville, UT 

Additional Author(s)

Harold T. Stokes, Brigham Young University Provo, UT 
Shae Machlus, Brigham Young U., Florida State U. Provo, UT 
Christopher Yost, Brigham Young University Provo, UT