Chemfig – How to Number Atoms

chemfigpositioning

I need to number atoms using chemfig. I thought I could use \chembelow and \chemabove to place numbers above and below but adding these commands changes the look of the drawing and does not simply only add the number.

\documentclass{minimal}
\usepackage{chemfig}
\begin{document}

\chemfig{*6(\chembelow{}{1}=\chembelow{}{5}-\chembelow{}{9}(*6(-=-=-=-=))--=\chemabove{}{2}-)}

\end{document}

Chemfig example

The lines are broken where the numbers are added. How can I add numbers without breaking the lines? Also, the numbers are placed very close — could that be related?

Best Answer

You can use invisible bonds:

\documentclass{article}
\usepackage{chemfig}
\begin{document}
\definesubmol\QQ{-[,0.2,,,draw=none]\scriptstyle}
\chemfig{*6((!\QQ1)=(!\QQ5)-(-[6,0.2,,,draw=none]\scriptstyle9)*6(-=-=-=)-[,,,,draw=none]-=(!\QQ2)-)}
\end{document}

connections between two molecules

If the question is how to draw connections between two molecules created with separate calls of \chemfig then the answer is in principle an easy one. ChemFig's molecules are TikZ pictures, really, and the atoms are nodes in this sense. As such they can be named through ChemFig's @{<node name>} syntax and connected afterwards through some \tikz[remember picture, overlay]...; or ChemFig's wrapper \chemmove{}.

The following example

\documentclass{article}
\usepackage{chemfig}
\begin{document}
General idea:\par
\chemfig{-[7]@{a}-[1]}

\vskip2em

\chemfig{-[1]@{b}-[7]}
\chemmove{ \draw[red,dotted] (a)--(b); }
\end{document}

gives after two compilations:

enter image description here

In your case, however, I don't think this is the best approach. In order to be able to connect the nodes they need to have unique names. If you use one node name repeatedly only the last instance is remembered:

As a consequence the method is not so nice when the nodes to be connected are hidden in repeated submols:

\documentclass{article}
\usepackage{chemfig}
\begin{document}

problem with molecules derived from submols:\par
\definesubmol{foo}{-[7]@{a}-[1]}
\definesubmol{bar}{-[1]@{b}-[7]}

\chemfig{!{foo}!{bar}!{foo}!{bar}}

\vskip2em

\chemfig{!{foo}!{bar}!{foo}!{bar}}
\chemmove{ \draw[green,dashed] (a)--(b); }

\end{document}

enter image description here

Finding the right atom

This addresses your second question:

Note that the red bond (emerging from OH in C6) is not properly placed. It should emerge from H instead than from O.

ChemFig provides a solution for this. Every bond in \chemfig{} has an optional arguments with five parameters:

-[<direction>,<length factor>,<departure>,<arrival>,<tikz options>]

The ones interesting here are <departure> and <arrival> which are integers specifying the numbers of the desired departure and arrival atoms. ChemFig's manual has the following example:

\documentclass{article}
\usepackage{chemfig}
\begin{document}

\chemfig{ABCD-[:75,,2,3]EFG}\qquad
\chemfig{ABCD-[:75,,,2]EFG}\qquad
\chemfig{ABCD-[:75,,3,2]EFG}

\end{document}

enter image description here

Proposed solution

In order to get two strands of cellulose I would suggest to save one submol of two glucoses with hydrogen bonds. Here's a possible definition using the turned-glucoBeta submol from my answer to the question you linked:

\definesubmol{bridged}{
  -[:10,.7,,,glycosid]4
  (
    -[:-10](-[:150,0.7]-[2,0.7]OH)
    -[:10]{\color{red}{O}}(-[:-8,1.2,,,bridge])
    -[:-50,.75]
  )
  -[:-50]
  (
    -[:170]HO
    -[6,,2,2,bridge]
    OH
    -[6,.7]
    -[:-30]
    -[:170]4(-[:-170,.475,,,glycosid])
    -[:-50](-[:170]HO)
    -[:10](-[:-50,.7]OH)
    -[:-10]1(-[6]H)(-[:10,.7,,,glycosid]{\color{glyc}O}!{turned-glucoBeta})
    -[:130]{\color{red}O}(-[:-8,1.2,,,bridge])
    -[:-170]
  )
  -[:10](-[:-55,0.7]OH)
  -[:-10]1(-[6,0.7]H)
  -[:10,.7,,,glycosid]{\color{glyc}O}
  !{turned-glucoBeta}
}

This submol can now be used repeatedly to get the polymer:

enter image description here

The full code

\documentclass[margin=.5cm]{standalone}
\usepackage{chemfig}
\tikzset{
  bridge/.style={dotted,blue} ,
  glycosid/.style={glyc}
}
\colorlet{glyc}{green}

\definesubmol{turned-glucoBeta}{
  -[:-10,.7,,,glycosid]4
  (
    -[:10](-[:-150,0.7]-[6,0.7]OH)
    -[:-10]{\color{red}{O}}-[:50,.75]
  )
  -[:50](-[:-170]HO)
  -[:-10](-[:55,0.7]OH)
  -[:10]1(-[2,0.7]H)
  -[:-10,.7,,,glycosid]{\color{glyc}{O}}
}
\definesubmol{bridged}{
  -[:10,.7,,,glycosid]4
  (
    -[:-10](-[:150,0.7]-[2,0.7]OH)
    -[:10]{\color{red}{O}}(-[:-8,1.2,,,bridge])
    -[:-50,.75]
  )
  -[:-50]
  (
    -[:170]HO
    -[6,,2,2,bridge]
    OH
    -[6,.7]
    -[:-30]
    -[:170]4(-[:-170,.475,,,glycosid])
    -[:-50](-[:170]HO)
    -[:10](-[:-50,.7]OH)
    -[:-10]1(-[6]H)(-[:10,.7,,,glycosid]{\color{glyc}O}!{turned-glucoBeta})
    -[:130]{\color{red}O}(-[:-8,1.2,,,bridge])
    -[:-170]
  )
  -[:10](-[:-55,0.7]OH)
  -[:-10]1(-[6,0.7]H)
  -[:10,.7,,,glycosid]{\color{glyc}O}
  !{turned-glucoBeta}
}
\begin{document}
\chemfig{!{bridged}!{bridged}!{bridged}}
\end{document}

Chemfig – How to Align Atoms with Chembelow/Chemabove?

a version showing all H, without using \chemabove or \chembelow

\setchemfig{atom style={scale=.85},atom sep=2.5em}
%
\chemname{\chemfig{C(-[2,.35,,,,draw=none]H)(-[:150]C(-[6,.35,,,,draw=none]H)(-[2,.35,,,,draw=none]H)-[:210]*6(=-=-=-))(-[:30]CH_3)-[:270]N(-[:210]H_3C)(-[:330]C(-[6,.35,,,,draw=none]H)(-[2,.35,,,,draw=none]H)-[:30]C~[:30]CH)}}
{Selegiline}
%

OR...

\setchemfig{atom style={scale=.85},atom sep=2.5em}
%
\chemname{\chemfig{C(-[2,.35,,,,draw=none]H)(-[:150]C(-[:70,.35,,,,draw=none]H_2)-[:210]*6(=-=-=-))(-[:30]CH_3)-[:270]N(-[:210]H_3C)(-[:330]C(-[:290,.37,,,,draw=none]H_2)-[:30]C~[:30]CH)}}
{Selegiline}
%

Best Answer

Related Solutions

Chemfig – Joining Atoms in Chemfig for Adjacent Molecules

connections between two molecules

Finding the right atom

Proposed solution

The full code

Chemfig – How to Align Atoms with Chembelow/Chemabove?

Related Question