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I need some cutoff radii to count bonds between different atoms in my system. When a .cif file is opened in Vesta, there are some default values of min and max bond lengths between two atomic species. While the minimum is always 0, the maximum values are different. How is this maximum value determined? Is it good enough cutoff to describe actual bonds in the system?

Screengrab of Edit> Bonds option in Vesta

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Minimum and maximum atomic distances can be selected by users. From the crystallographic point of view the nearest neighbour distances depend on the atomic sizes of the involved elements (C-C distance is shorter than U-U distance, for example).

In any case, the best thing is to plot the structure; then, you can measure the distance between selected atoms using the "Distance" tool in the vertical panel on the left (see the image). At this point you have an idea of the distange range and you can select the minimum and maximum atomic distances to be considered in the "bonds" window.

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  • $\begingroup$ thanks for your response. What I was particularly interested to know was how do VESTA set the default maximum bond lengths? For example, in case of Ba-O bonds, the default maximum is always 3.14795 A. How do they arrive at such a particular value? $\endgroup$
    – rik
    Jan 4, 2023 at 18:42
  • $\begingroup$ What do you mean with " in case of Ba-O bonds, the default maximum is always 3.14795 A"? Is this true also for other structures? I don't know how Vesta select the default values. I guess it could use 2 different approaches. 1) takes into account the atomic sizes of the involved elements; 2) determines the distances between the atomic species using the crystallographic data. $\endgroup$
    – gryphys
    Jan 5, 2023 at 11:28
  • $\begingroup$ It is true for all structures. The bond length min and max are fixed for any two pair in VESTA. I think your approach is fundamentally what needs to be done. But then we have to decide whether to use ionic radius/covalent radius, and decide the coordination number(because ionic radius depends on it). But to find coordination number from a structure, we need to know the radius to consider. So it sort of becomes a chicken-and-egg problem? $\endgroup$
    – rik
    Jan 6, 2023 at 14:28
  • $\begingroup$ @rik I cannot agree. Bond length is calculated by using atomic positions and lattice parameters. Ionic or covalent size do not matter, the distance will be always the same because it is between the centers of the atoms, not between their surfaces. To determine the coordination number, you must look at your structure and play with it. In any case ionic radii as those given by Shannon hold also for covalent structures. $\endgroup$
    – gryphys
    Jan 8, 2023 at 19:49
  • $\begingroup$ BTW, ionic radii (for example those determined by Shannon) hold also for covalent structure. In the end, no purely ionic bond is known, a signifant percentage of covalent bonding is always present. $\endgroup$
    – gryphys
    Jan 8, 2023 at 19:54

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