Analysis of a hydroquinone polymorph 


Algorithm:

1. Open the database C6H6O2 and compute the adjacency matrices for all the 11 compounds of C6H6O2 composition considering hydrogen bonds (AutoCN Method: Domains).

2. Go to the second record in the list (Ref. Code HYQUIN), open the Crystal Data window and be sure that this is a hydroquinone polymorph.

Press Calculate button and find that the composition of the unit cell corresponds to the composition of hydroquinone. Press Yes button.

3. Open the window of the program IsoCryst (Programs/IsoCryst). Perform the following operations:
  • Display one unit cell clicking on the yellow pencil button .

  • 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 . 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 .

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

  • Move the image with the tools Rotate - Z Rotate - Magnify/Shrink - Translate .

  • 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.

    Click on the button to use the Select tool. Select one group of atoms connected together. For this purpose push/activate the button select polymeric chain” and then click on an atom, all the others connected to it will be selected and shown/coloured in yellow. This will immediately show if a compound is made of 0D, 1D or 3D subnets.

  • Choose to display only the selected subnet clicking on (Show selection only) and display both the atom names and the bond/interaction distances with a click on some of the buttons on the bottom left: (Atoms labels) and (Show Bond Distances). Click on button to show unselected atoms.

  • Show different kinds of bonds/interactions. You have to go into the Options window following Image/Options, or click on up right button . Go to Bonds tab and select which kind of interaction to visualize, e.g. hydrogen bonds (Show column). Press Ok.

    The hydrogen bonds are dot-dashed.

  • Click on and release and . Then open the Options window again. Check Hydrogen bonds box in the Take column to consider hydrogen bonds as possible growth of the network.

    Press Ok and perform one time the Growth operation to show the atoms connected with the selected molecule by hydrogen bonds.

    Now uncheck Hydrogen bonds box, unselect the molecule by right-clicking on any of its atoms or on an empty space in the window and perform the Growth operation a few more times to show the molecules connected with the selected molecule by hydrogen bonds.

    Check Hydrogen bonds box again and grow the net. Then press Space key or button to fit the view to the window size. Rotate the image to be sure that the net is 2D.

    Press Undo button several times to go back to the previous view.

  • To compute distances, bond or dihedral angles toggle on selection mode and select pairs, triples or quadruples of atoms and read the value in the status line. For example below the angle for the hydrogen bond O2–H4…O2 is equal to 154.23° (see status line at the bottom of the window) To compute a dihedral angle between two RMS planes select the atoms lying in one plane (yellow selection) and then select atoms of the other plane holding Ctrl key (magenta selection). Thus, the dihedral angle between two hydroquinone molecules is equal 66.79°. To unselect the magenta selection hold Ctrl key and right-click on atoms or on an empty space in the window.

  • Select a hydroquinone molecule in yellow and click on button. A molecular Voronoi-Dirichlet polyhedron will be constructed . Open the Information window by selecting Calculate/Selected Atoms and find the volume of the molecule in the solid (V = 131.99 or 132.88 Å3 for two nonequivalent molecules). Click Ok to close the window

    Now unselect the molecule, to get the following picture

    Remove the Voronoi-Dirichlet polyhedron by clicking button.
4. Close the IsoCryst window.

Exercise: analyze your own structures with IsoCryst.

Hints: Play with the other button on the bottom bar:

Increase Atom radius. Change Radii System to Sph. Domain to get the atom size close to fill the space. With a bit of play you can get CPK picture-like as shown below.

Show Vertices and Fill Faces, take effect on the Voronoi-Dirichlet polyhedron.


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