I would like to draw the following structures: enter image description here

How many I do it?

  • $\begingroup$ You have two options: (a) either draw these structures on your own using your choice of visualization software, or (b) You can request permissions to reuse them. In most of the cases you would get the license free of charge, if you are an academic, and wants to use it in a different publication. $\endgroup$ Feb 19 at 17:12
  • $\begingroup$ @HemanthHaridas thank you for your answer, please can you give me the name of the software to draw it. $\endgroup$
    Feb 19 at 17:20

2 Answers 2


Following the answer by @NikeDattani, you can also search the Wikipage for each compound and look for this part (this is for Li2S):

enter image description here

There you will find the links for databases with information about the compound and usually the 3D structure file is available to download.


In order to draw those chemical structures with , the software needs to know (or be able to calculate) the coordinates of each type of nucleus.

Usually the software would be provided with an XYZ file, for example if the molecule is pyridine, an appropriate XYZ file would be the following:

C       -0.180226841      0.360945118     -1.120304970
C       -0.180226841      1.559292118     -0.407860970
C       -0.180226841      1.503191118      0.986935030
N       -0.180226841      0.360945118      1.29018350
C       -0.180226841     -0.781300882      0.986935030
C       -0.180226841     -0.837401882     -0.407860970
H       -0.180226841      0.360945118     -2.206546970
H       -0.180226841      2.517950118     -0.917077970
H       -0.180226841      2.421289118      1.572099030
H       -0.180226841     -1.699398882      1.572099030
H       -0.180226841     -1.796059882     -0.917077970

With this information, the software knows where to put each nucleus, and what color to make each nucleus.

is a free and open source software that can make figures like the ones in your question. My research group has primarily been using Avogadro to make such figures: We have had issues with making vector format PDF or SVG files with transparent backgrounds, but the software is free and open source and does well for the most part. If you look at the tag, you will see that many other computers programs can also be used as alternatives. We have also used GaussView, VMD and some other visualization programs.

  • $\begingroup$ Surely if you've got an SVG (or indeed a PDF) you can just delete the background in Inkscape (or even with a script to delete any style="background-color..." tags if they're used? Then it becomes a case of how well the software in which you're using your vector graphics handles transparency. For a partially transparent background you might want to delete and re-add $\endgroup$
    – Chris H
    Feb 20 at 15:32
  • $\begingroup$ @ChrisH My recollection is that the shading of the spheres (the spheres that represent nucleii) was not as good when exported to SVG or PDF format, so we used PNG files for our manuscripts. Before these "manuscripts" become "publications", I would indeed like to have vector graphics instead of PNG rasters, but my recollection is that the students that were working on it, could not achieve this yet. $\endgroup$ Feb 20 at 22:59
  • $\begingroup$ I'll have to take a look. It's possible the output uses transparency gradients, which not everything handles well, but normal gradients for sphere shading would make more sense even with a transparent background. $\endgroup$
    – Chris H
    Feb 21 at 6:39

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