# How to illustrate an isomerisation mechanism with chemfig

I'd like to produce a scheme of the isomerisation mechanism of hop alpha-acids during wort boiling in beer as featured in Verzele, 1986. (Don't worry, I'll post the link for the article). I'd like to reproduce clearly the mechanism of Figure 5 (p. 34 or the 3rd page if you prefer). It looks shitty when I wanted to include the figure, plus it seems weird since the rest of my figures have been produce with \chemfig.

The only challenge that I have is to ad the arrows to structure V of the figure and put \ominus on the side instead floating next to an atom of oxygen.

Here's what I've done so far for structure V:

\chemfig{*6((-HO)-(([:240]<:HO)(<[:300]-[:270]=[:330](-[:30])-[:270]))-(-[,,,,,lddbond]O)-[,,,,,rddbond](-[:30,,,,,lddbond]([:90,,,,,lddbond]-O)-[:330]R)-[,,,,,rddbond](-[,,,,,rddbond]O^{\ominus})-(-[:150]-[:210]=[:150](-[:90])-[:210])=)}


Here's the link of the article: http://onlinelibrary.wiley.com/doi/10.1002/j.2050-0416.1986.tb04372.x/pdf

• Welcome to TeX.sx! You mean placing the formal charge symbol in between the two oxygens? Should easily be possible with an invisible bond (-[,,,,draw=none]). For more concrete help a compilable example would be helpful (how did you define the TikZ style rddbond? for example...) Jun 23 '15 at 7:42
• I don't think I defined the "rddbond" but it works though. The bond appears and are ok but they disappear when I add the arrows for the isomerisation reaction of humulone. I can either have one of them, but I need both. The image of the original text is so blurry and I'd love to illustrate it better in my thesis. P.S. I also tried what you suggested (-[,,,,draw=none]) and it also didn't work. Jun 25 '15 at 17:43
• rddbond is not e predefined TikZ style. I vaguely remember that there's an example in the chemfig manual which defines it. You must have a definition for it in your document of you'd get some kind of error. More importantly: if you want concrete help I'd really appreciate if you'd add a minimal working example (a short (!) but complete and compilable document code starting with \documentclass and ending with \end{document}) to your question Jun 26 '15 at 10:24
• Here's my code. I have no problem now with the double dash bonds. The only problem is with when I want to recreate structure 3 and 4 in the picture attached to this message. There's always a problem when I want to draw the arrows to one bond or one atom to another. Either the ring structure is altered, the angles of branched chains are not displayed correctly or the arrow point to the atom and not the bond of the atom. Anyway, sorry for the delay. I've never had a notification of your reply but thanks for the TiKZ style info. It helped a lot! [![enter image description here](i.stack.img Aug 6 '15 at 4:58

Taken the code from the other answer (and not verifying if the formulae match the picture) I came up with the following. For the numbering I use the chemnum package (but you should use more meaningful names than me, I chose one, two, three…). For formal charges, the cis/trans nomenclature and the molecules on the arrows I use the chemmacros/chemformula packages. The package showframe is used to visualize page dimensions.

\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[english]{babel}
\usepackage{chemfig}

\usepackage{chemnum,chemmacros}

\usetikzlibrary{decorations}
\pgfdeclaredecoration{ddbond}{initial}{
\state{initial}[width=4pt]{
\pgfpathlineto{\pgfpoint{4pt}{0pt}}
\pgfpathmoveto{\pgfpoint{2pt}{2pt}}
\pgfpathlineto{\pgfpoint{4pt}{2pt}}
\pgfpathmoveto{\pgfpoint{4pt}{0pt}}
}
\state{final}{
\pgfpathlineto{\pgfpointdecoratedpathlast}
}
}
\tikzset{lddbond/.style={decorate, decoration=ddbond}}
\tikzset{rddbond/.style={decorate, decoration={ddbond, mirror}}}

\usepackage{showframe}

\begin{document}

\begin{center}
\scriptsize
\setchemfig{
atom sep = 1.2em,
cram width = .3em,
bond offset = .1em
}
\schemestart
% 1
\chemname{\chemfig{*6((-HO)-(([:240]-(-[:270]=[:210](-[:150])-[:270]))(-[:300]-[:270]=[:330](-[:30])-[:270]))-(=O)-(-[:30]([:90]=O)-[:330]-[:30](-[:90])-[:-30])=(-OH)-(-[:150]-[:210]=[:150](-[:90])-[:210])=)}}{\cmpd{one}}
\arrow{0}[,.5]
% 2
\chemname{\chemfig{*6((-HO)-(([:240]<:HO)(<[:300]-[:270]=[:330](-[:30])-[:270]))-(=O)-(-[:30]([:90]=O)-[:330]-[:30](-[:90])-[:-30])=(-OH)-(-[:150]-[:210]=[:150](-[:90])-[:210])=)}}{\cmpd{two}:
Humulone}
\arrow{->[\ch{OH-}][$\Delta$]}[,1.5]
% 3
\chemname{\chemfig{*6((-[:-150]O-[:180]H)-(([:240]<:HO)(<[:300]-[:270]=[:330](-[:30])-[:270]))-(-[,,,,,lddbond]O)-[,,,,,rddbond](-[:30,,,,,lddbond]([:90,,,,,lddbond]-O)-[:330]-[:30](-[:90])-[:-30])-[,,,,,rddbond](-[,,,,,rddbond]O|^{\fminus})-(-[:150]-[:210]=[:150](-[:90])-[:210])=)}}{\cmpd{three}}
\arrow{->[*0\ch{H+}]}[-90]
% 4
\chemname[3.5ex]{\chemleft[
\chemfig{*6((=O)-(([:240]<:HO)(<[:300]-[:270]=[:330](-[:30])-[:270]))-(-[,,,,,lddbond]O)-[,,,,,rddbond](-[:30,,,,,lddbond]([:90,,,,,lddbond]-O)-[:330]-[:30](-[:90])-[:-30])-[,,,,,rddbond](-[,,,,,rddbond]O^{\fminus})-(-[:150]-[:210]=[:150](-[:90])-[:210])-)}
\chemright]}{\cmpd{four}: ketonized anion intermediate}
\arrow[-180]
% 5
\chemname{\chemfig{*5((<:(-[::60](=[::60]O)-[::-60]-[::60]=[::-60](-[::-60])-[::60]))(<HO)-(-OH)=(-(=[:60]O)-[:-60]-(-[:60])-[:-60])-(=O)-(<:[::-54]-[::+60]=[::-60](-[::-60])-[::+60])-)}}{\cmpd{five}:
\trans-isohumulone}
\arrow{0}[-180,.5]
\chemname{\chemfig{*5((<(-[::60](=[::60]O)-[::-60]-[::60]=[::-60](-[::-60])-[::60]))(<:HO)-(-OH)=(-(=[:60]O)-[:-60]-(-[:60])-[:-60])-(=O)-(<:[::-54]-[::+60]=[::-60](-[::-60])-[::+60])-)}}{\cmpd{six}:
\cis-isohumulone}
\schemestop
\end{center}

\end{document}
`