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4

I am quite certain that this issue arises due to the vertical placement mechanism of the chemfig package. Specifically, the chemfig manual (v1.2d, December 1, 2015, currently latest) specifically states that [...] the vertical placement of the arrival atom depends on the height of the departure atom. [...] ChemFig adds to each arrival atom the \vphantom ...

2

Apparently, the problem arises because of the glossary entry \gls{DPPM} on the second arrow: During the first (invisible) invocation on the arrow, \gls{DPPM} gets rendered as the long Bis"-(di"-phenyl"-phos"-phino)"-methan (DPPM) as defined in the glossary file. This causes a line break and a larger height of the (invisible) bounding box in the first frame, ...

1

Do you want something like this? \documentclass{scrbook} \usepackage{wrapfig} \usepackage{chemfig} \usetikzlibrary{fit} \usepackage{kantlipsum} \newcommand{\namemole}[1][]{% \chemfig{% ...

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