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I have optimized the structure of diborane with Gaussian at the B3LYP/6-31+g(d,p) level and when check it on Gaussview I found that there are two hydrogens with no bond to boron atoms (like free atoms) and the two B atoms are bonded. Frequency calculations gives zero imaginary frequencies and when I compute properties (like ionization potential) the values are good approximations.

I wonder if the problem is with the calculation or only the graphical interface of Gaussview doesn't recognize it as an actual bond.

Also, the bond distances are in accordance with the literature (~1.3 Angstroms for H shared between the borons and ~1.19 Angstroms for the others).

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  • $\begingroup$ Welcome to Chemistry.SE! Take the tour to get familiar with this site. Mathematical expressions and equations can be formatted using $\LaTeX$ syntax. I find it highly likely that the distance exceeds to preset parameter in Gview and hence it is not displayed as a bond. It would be helpful if you could add the optimised geometry (as xyz coordinates) and the absolute energy for members to reproduce the situation. In the meantime I recommend trying to view the compound with a different software, e.g. molden, avogadro, etc... $\endgroup$ – Martin - マーチン Jul 27 '16 at 8:51
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    $\begingroup$ Roughly speaking, there are no such things as bonds. There is molecular geometry, and if it is realistic, then what's the problem? Use the visualization software of your choice to draw the sticks wherever you like them. $\endgroup$ – Ivan Neretin Jul 27 '16 at 9:55
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I wouldn't put too much faith in the representation of bonding in GaussView, it's simply determined by bond distances and often it doesn't show the bond at all for some unknown reason. If your geometry is good, then you can use your knowledge and intuition of bonding to recall the true structure.

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As mentioned GaussView as do many other visualizers use distances and angles to determine bonds. If you want bonding information, you need to resort to atoms in molecules or natural bond order calculations. Assuming you are using Gaussian, the latter is available via the NBO keyword.

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  • $\begingroup$ I'll update this with links when I'm not on a phone. $\endgroup$ – Deathbreath Jul 29 '16 at 16:45

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