Analysis of the crystal structure of β-UO2SO4 


Algorithm:

1. Open the database UO2SO4 that contains one record corresponding to β-UO2SO4 and compute the adjacency matrix with the AutoCN program (Method: Domains).

3. Run IsoCryst (Programs/IsoCryst). Or click the button

4. Perform the following operations with the crystal structure image:
  • Press to draw the unit cell composition.

  • Grow the network (i.e. extend the content of the unit cell by the atoms connected to the one inside the cell). Use the command Ctrl+W or push the button one time. The image looks as follows

  • Click on the button or on the button to choose the OpenGL or API modes, respectively.

  • Try different plot styles: Wire - Cylinder - Sphere & Wire - Sphere & Cylinder .

  • Try coloured bonds versus uncolored (white)

  • Toggle on/off: Show crystal axes - Show legend - Show cell edges .

  • Move the image with the tools Rotate - Z Rotate - Magnify/Shrink - Translate . To rotate or magnify by a precise value, double-click the tool icon and enter the value.

  • Some of the other bottom buttons allow to display/orient the view according to some predefined directions/projection defined by the crystallographic hkl: , or (along the axis a, b or c).

    Clicking on you should specify the hkl values for the direction on which to project the view, for example 1,0,1 or 0,-1,3 etc.

  • Show atom names by clicking the button .

  • Click on the button to use the Select tool. Select one of uranium atoms and leave it alone on the picture by pressing the button .

  • Grow the structure one time by clicking and put the image into the centre by pushing the Space key.

  • Draw the coordination polyhedron for the uranium atom (it should be selected) by clicking . Remove the polyhedron using the button .

    Compute interatomic distances U–O. For this purpose, having selected an uranium atom, select oxygens one-by-one, every time unselecting the previous oxygen. Read the distance value in the status line. For example, (O1-U1) r = 2.361 Å, (O5-U1) r = 1.796 Å

  • Compute bond angles O–U–O by selecting triples of atoms. What are the angle values for equatorial and apical oxygens? For example, angle (O5-U1-O6) = 176.11° for apical, and 83.76° for equatorial.

  • Unselect all atoms by right-clicking in an empty space of the window.

  • Compute the root-mean-square deviation (σ) from the RMS plane for equatorial oxygens of the uranium coordination shell including the uranium atom. For this purpose, select all these atoms and perform the Calculate/Selected Atoms command. The resulting value should be σ = 0.15Å. Compute the distance from the uranium atom to the RMS plane by magenta-selecting the atom (holding Ctrl key). You should select oxygen atoms of the equatorial plane by yellow (left click) and uranium atom by magenta (left click + Ctrl key) The resulting value in the status line should be equal 0.0492Å. Unselect all atoms by right-clicking in an empty space of the window.

  • Compute the angle between equatorial plane of the uranium coordination polyhedron and the uranуl O–U–O group. You should select oxygens of the equatorial plane and uranуl group by yellow and magenta, respectively. The resulting value should be 88.80°.

  • Restore the initial image by clicking .

  • Perform the Growth command one time. Select all atoms in a sphere of radius 3Å around one of the uranium atoms. For this purpose, set the sphere selection mode , select an uranium atoms and left-drag the sphere of required radius. You should have 8 atoms selected. Click to leave visible the selected atoms only.

    Perform the Growth command one time and compute the torsion angles O–U–O–S. Find the angle equal to 148.08°. Answer: O3-U1-O2-S1.

  • Compute the angle between equatorial planes of a pair of uranium atoms connected via bridge oxygen atom. For this purpose, select the oxygen atoms of the two planes in yellow and magenta. The resulting value should be equal 61.16°.

  • Restore the initial image by clicking and perform the Growth command several times.

  • Select chains of the uranium coordination polyhedra connected by vertices (oxygen atoms). For this purpose, draw the legend by clicking the button, then select in magenta all sulfur atoms by clicking the sulfur atom in the legend holding the Ctrl button. Remove the selected sulfur atoms by pressing the Delete button. Then select all atoms in a chain by specifying the selection mode and clicking any atom of the chain.

  • Restore the initial image by clicking and perform the Growth command several times.

  • Select pseudo-layers by removing O(2) atoms. For this purpose, choose the “Magic Wand” tool , click one of the O(2) atoms and specify Command: Delete, Do for: Cryst. Sort. Select one layer and leave it alone on the image. Arrange the layer perpendicular to [001] using the button . Restore the initial image.

    Select other pseudo-layers by removing O(3) atoms. What direction is perpendicular to them? Answer: (100)

  • Restore the initial image and perform the Growth command several times. Select all uranium and sulfur atoms and draw the structure in a polyhedral representation using the button . Try different options for drawing polyhedra in the IsoCryst options window (use the button , the Polyhedra tab).

  • Remove polyhedra from the image, select all uranium atoms and remove them. Use Undo command (the button ) to cancel the removal.

  • Close the IsoCryst window.


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