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Here is my kludge to solve this: \begin{array}{c} \chemfig{ H_{3}\chemabove{N}{\scriptstyle+}- CH( -[:90,,1,1]R^{1} )- C( =[:-90]O )- OH \qquad + \qquad H- N( ...

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The parentheses ( and ) are special characters inside \chemfig. They denote branching (and also are part or the ring syntax). \chemfig{(Si)} starts a branch after an empty atom which in effect seems to shift the baseline. \documentclass{article} \usepackage{chemfig} \begin{document} X\chemfig{H-C-H}X\chemfig{C}X \par X\chemfig{-C-}X\chemfig{(C)}X \end{...

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As I'm sure you know when you have used chemfig already the bonds have optional arguments. The manual says: 6 Customization of bonds There is a fifth and last optional argument for bonds which is found after the fourth comma: [,,,,<tikz code>] This means all you have to do is adding the TikZ code for an arrow: \documentclass{article} \...

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The undefined control sequence error pointing to \mcfcringle indicates that the mol2chemfig.sty file is not being found. Because mol2chemfig is not packaged with either TexLive or MikTeX you will need to install it manually. See the TexLive or MikTex manual for details on how to do this. After downloading mol2chemfig.sty from here: http://chimpsky.uwaterloo....

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