Angstrom circle not centred

The left-offset of the ångström symbol is caused by tgbonum. You can fix this by also loading usepackage[T1]{fontenc} after tgbonum.

I also suggest that you use siunitx‘s provided macro (instead of only using the package to obtain the unit), SI, to properly typeset values with units:

$approx SI{3.5}{angstrom}$

With the OT1 encoding, r{A} is a predefined combination that doesn’t use the ring accent, but uses a more complex setup, because the ring should be attached to the A. This setup fails with TeX Gyre Bonum, but it can be fixed.

I also suggest to scale down the font, because it has a rather large x-height; alternatively, you could increase the leading with linespread{1.1} or similar.

You can get numbers with SI in the text font by using mode=text.

documentclass{article}
usepackage[scale=0.94]{tgbonum}
usepackage[mode=text]{siunitx}

makeatletter
DeclareTextCompositeCommand{r}{OT1}{A}{%
  leavevmodevbox{%
    offinterlineskip
    ialign{hfil##hfilcrchar23crnoalign{kern-1.15ex}Acr}%
  }%
}
makeatother

begin{document}

r{A}ngstrom or AA ngstrom r{A}r{U} r{a}r{u}

Additionally, it is accompanied by a drastic change in
end-to-end distance of~SI{3.5}{angstrom} as well as polarity
(3~Debye for emph{cis} versus 0~Debye for emph{trans}).

end{document}

Note that using $word$ is not the way to get italics.

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