Spacing – Spacing and Fitting a Big Reaction Mechanism with Chemfig

chemfigspacing

I want to replicate the following reaction mechanism:

Problems are:

Arrows are not middle centered to the compounds
Vertical and horizontal spacing is insufficient and unequal
Names appear at different distances
I ignore how to make everything fit inside the margins in a centered way (already tried \begin{small} \end{small} and until atom sep=0.1cm)

I thought \hspace{1em} would help, that is why I added it after each compound and arrow. I assigned a letter to each compound:

a = Q

b = 14THQ

c = DHQ

d = PCHA

e = PCHE

f = PCH

g = 58THQ

h = OPA

i = PB

This is my code:

\documentclass{article}
\usepackage[version=4]{mhchem}
\usepackage{mol2chemfig}
\setchemfig{atom sep=0.8cm}
\begin{document}

\begin{center}
\schemestart[0,1,thick]
\chemname{\chemfig{=^[:270]-[:330]=^[:30]-[:90](=^[:150]-[:210])-[:30]=_[:330]-[:270]=_[:210]N(-[:150])}}{Quinoline}\hspace{1em}
\arrow(a--b){<=>}[,0]\hspace{1em}
\chemname{\chemfig{-[:150]-[:210]=^[:150]-[:210]=^[:270]-[:330]=^[:30](-[:90])-[:330]\mcfbelow{N}{H}-[:30](-[:90])}}{14THQ}\hspace{1em}
\arrow(@b--c){<=>}[-90,0]\hspace{1em}
\chemname{\chemfig{-[:270]-[:330]-[:30]-[:90](-[:150]-[:210])-[:30]-[:330]-[:270]-[:210]\mcfbelow{N}{H}(-[:150])}}{DHQ}\hspace{1em}
\arrow(@c--d){<-}[,0]\hspace{1em}
\chemname{\chemfig{NH_2-[:150,,1]-[:210]-[:150]-[:90]-[:30]-[:330](-[:270])-[:30]-[:330]-[:30]}}{PCHA}\hspace{1em}
\arrow(@d--e){<-}[,0]\hspace{1em}
\chemname{\chemfig{-[:180]-[:120]-[:180]=_[:240]-[:180]-[:120]-[:60]-(-[:300])}}{PCHE}\hspace{1em}
\arrow(@e--f){<-}[,0]\hspace{1em}
\chemname{\chemfig{-[:180]-[:120]-[:180]-[:240]-[:180]-[:120]-[:60]-(-[:300])}}{PCH}\hspace{1em}
\arrow(@c--g){<=>}[180,0]\hspace{1em}
\chemname{\chemfig{-[:30]-[:90](-[:150]-[:210]-[:270]-[:330])-[:30]=_[:330]-[:270]=_[:210]N(-[:150])}}{58THQ}\hspace{1em}
\arrow(@g--){<=>}[90,0]\hspace{1em}
\arrow(@b--h){<-}[,0]\hspace{1em}
\chemname{\chemfig{-[:180]-[:120]-[:180]=_[:240]-[:180]=_[:120]-[:60]=_(-[:300])-[:60,,,1]NH_2}}{OPA}\hspace{1em}
\arrow(@h--i){<-}[0,0]\hspace{1em}
\chemname{\chemfig{-[:180]-[:240]-[:180]=^[:120]-[:180]-[:240]-[:300]-(-[:60])}}{PB}\hspace{1em}
\schemestop
\end{center}

\end{document}

And this is my ugly result:

Best Answer

To make this kind of reaction mechanism, it is best to use the chemfig program. Chemfig package

I put the name of the molecules using markers, and invisible arrows, instead of using the \chemname command.

\documentclass[margin={2mm 2mm}]{standalone}
\usepackage{tikz}
\usepackage{chemfig}

\begin{document}
\schemestart
%
\chemfig{*6(-=@{a}*6(-N=-=-)-@{c}=-=)}
%
\arrow{<=>}
%
\chemfig{*6(-=@{b}*6(-\chembelow{N}{H}----)-@{d}=-=)}
%
\arrow{->}
%
\chemfig{*6(-=(-NH_2)-@{e}(-[:30]-[:330]-[:30])=-=)}
%
\arrow{->}
%
\chemfig{*6(-=-@{f}(-[:30]-[:330]-[:30])=-=)}
%
\arrow(@{a}--){0}[270,.2]{}\arrow{<=>}[270,1.5]
%
\chemfig{*6(--@{g}*6(-N=-=-)----)}
%
\arrow{<=>}
%
\chemfig{*6(--@{h}*6(-\chembelow{N}{H}----)----)}
%
\arrow{->}
%
\chemfig{*6(--@{i}(-NH_3)-(-[:30]-[:330]-[:30])---)}
%
\arrow{->}
%
\chemfig{*6(-@{j}-=(-[:30]-[:330]-[:30])---)}
%
\arrow{->}
%
\chemfig{*6(-@{k}--(-[:30]-[:330]-[:30])---)}
%
\arrow(@{b}--){0}[270,.2]{}\arrow{<=>}[270,1.5]
%-----------------------------------------
\arrow(@{c}--){0}[90,.4]\parbox{.5cm}{\textbf{Q}}
\arrow(@{d}--){0}[90,.4]\parbox{1cm}{\centering{\textbf{14THQ}}}
\arrow(@{e}--){0}[90,.4]\parbox{1cm}{\centering{\textbf{OPA}}}
\arrow(@{f}--){0}[90,.4]\parbox{1cm}{\centering{\textbf{PB}}}
%
\arrow(@{g}--){0}[270,.4]\parbox{1cm}{\centering{\textbf{58THQ}}}
\arrow(@{h}--){0}[270,.4]\parbox{1cm}{\centering{\textbf{DHQ}}}
\arrow(@{i}--){0}[270,.4]\parbox{1cm}{\centering{\textbf{PCHA}}}
\arrow(@{j}--){0}[270,.1]\parbox{1cm}{\centering{\textbf{PCHE}}}
\arrow(@{k}--){0}[270,.1]\parbox{1cm}{\centering{\textbf{PCH}}}
%
\schemestop
\end{document}

Related Solutions

[Tex/LaTex] Drawing Benzene resonance mechanism, and reaction mechanism + curly arrows

chemfig allows to add explizit node names to either bonds or atoms in its formulae by using the @{<name>} syntax. These names can be used in a tikzpicture with the options remember picture, overlay to draw the curved arrows. chemfig provides the wrapper \chemmove for this. So a combination of chemfig and TikZ can be used to draw the schemes. (BTW: the chemfig manual actually has quite a few examples of such schemes...)

Here is something that might get you started:

\documentclass{article}
\usepackage{chemfig}
\tikzset{
  elmove/.style={->,shorten >=3pt, shorten <=3pt}
}
\begin{document}

\schemestart
  \chemfig{*8(-[@{sb1}]=[@{db1}]-[@{sb2}]=[@{db2}]-[@{sb3}]=[@{db3}]-[@{sb4}]=[@{db4}])}
  \arrow{<->}
  \chemfig{*8(=-=-=-=-)}
\schemestop
\chemmove[red,elmove]{
  \draw (db1) .. controls  +(90:5mm) and  +(45:5mm) .. (sb1) ;
  \draw (db2) .. controls +(180:5mm) and +(135:5mm) .. (sb2) ;
  \draw (db3) .. controls +(270:5mm) and +(225:5mm) .. (sb3) ;
  \draw (db4) .. controls   +(0:5mm) and +(315:5mm) .. (sb4) ;
  % similar the others
}

\bigskip

\schemestart
  \chemfig{**6(----[@{b}]--)}
  \arrow(benzene.base east--.base west){->[][][15pt]}
  \chemfig{**[120,420,dashed]6(---(-[,-1,,,draw=none]{+})-(-[:120]H)(-[:60]NO_2)--)}
  \arrow(@benzene.45--){0}[45,.2]
  \chemfig{@{N}\chemabove{N}{+}O_2}
\schemestop
\chemmove[blue,elmove]{
  \draw[shorten <=-5pt] (b) .. controls +(30:5mm) and +(-90:1cm) .. (N) ;
}

\end{document}

enter image description here

My package modiagram can be used to draw the electronic state diagram. IMHO It doesn't fit perfectly and a TikZ-only solution may be preferable. On the other hand the code is rather easy:

\documentclass[11pt]{book}
\usepackage[utf8]{inputenc}
\usepackage{chemformula,modiagram,chemfig}

% necessary due to stupid bug in `modiagram':
\newcommand*\makecolonother{\catcode`\:=12 }

\begin{document}
\ch{_4Be}: 1s$^2$~2s$^2$

ground state:
\begin{MOdiagram}[style=square,AO-width=8pt]
  \AO(0pt){s}{0;pair}
  \AO(12pt){s}{0;pair}
  \AO(24pt){s}{0;}
  \AO(34pt){s}{0;}
  \AO(44pt){s}{0;}
  \draw[overlay,red,->]
    (AO2.north) .. controls +(0,.5) and +(0,.5) .. (AO3.north) ;
\end{MOdiagram}

excited state:
\begin{MOdiagram}[style=square,AO-width=8pt]
  \AO(0pt){s}{0;pair}
  \AO(12pt){s}{0;up}
  \AO(24pt){s}{0;up}
  \AO(34pt){s}{0;}
  \AO(44pt){s}{0;}
  \makecolonother
  \draw[<-,overlay]
    (AO2.south) -- ++(-100:3mm) node[below] {Cl} ;
  \draw[<-,overlay]
    (AO3.south) -- ++(-80:3mm) node[below] {Cl} ;
\end{MOdiagram}

\end{document}

enter image description here

[Tex/LaTex] chemfig: reaction above arrow

As I understand the question, the problem is in the "label" of the arrow and how to do the "circle" with arrows. One way to do this is to play with the properties of chemmove and the arrows.

For example:

\schemestart
\chemfig{First molecule}
\arrow{->[
\chemname[24pt]{\chemfig{N@{st1}ADH}}{\scriptsize \parbox[c]{40pt}{\centering ammonium formate}}
\hspace{0.5cm}
\chemname[24pt]{\chemfig{N@{en1}AD}}{\chemfig{CO_2}}
\chemmove{\draw[->,shorten <=5pt, shorten >=5pt](st1) .. controls +(+50:8mm) and +(+130:8mm)..(en1);}
\chemmove{\draw[->,shorten <=5pt, shorten >=5pt](en1) .. controls +(-130:8mm) and +(-50:8mm)..(st1);}
\chemmove{\draw[->,shorten <=5pt, shorten >=5pt,transform canvas={yshift=-32pt}](st1) .. controls +(+50:8mm) and +(+130:8mm)..(en1);}
]}[,2.4]
\chemfig{second molecule}
\schemestop

Note that maybe further adjusting of the spaces is required.

Best Answer

Related Solutions

[Tex/LaTex] Drawing Benzene resonance mechanism, and reaction mechanism + curly arrows

[Tex/LaTex] chemfig: reaction above arrow

Related Question