[Tex/LaTex] How to make a chemical diagram with mhchem

mathjaxmhchem

I need to write two symbols one below the other, and I referred to the following posts:

How to write something vertically below another math symbol

How to write below/above the text in LaTeX?

However, using \underset{}{} or \stackrel{}{} decreases the size of one symbol with respect to the other. underset{}{} makes the bottom symbol smaller, and \stackrel{}{} makes the top smaller (Go to the bottom of the page here to test it out)

My Question: Is there any LaTeX or MathJax command that stacks two things symbols but does not change the size of either one?

My Use: I want to use it to make a simple organic chemistry molecule (2-methyl 2-chloro propane). The closest I have come to rendering it approximately the same size is

\ce{CH3\bond{1}}
{\stackrel{
   \;\;\;\large\ce{CH3}
}{\stackrel{|}{\underset{\underset{\huge\ce{Cl}}{|}}{\ce{C}}}}}\ce{-CH3}

(Go to the bottom of the page here to test it out)

It is extremely messy, but still not the same size. Please don't ask me to use chemfig, there are a few reasons I don't want to use it.

Best Answer

There are several packages in LaTeX that will produce chemical diagrams. See this post and its answers for an overview.

As an example, using chemfig (even though you want to avoid it) the diagram can be produced using the following code:

\documentclass{article}
\usepackage{chemfig}

\begin{document}

\chemfig{CH_3-C(-[2]CH_3)(-[6]Cl)-CH_3}

\end{document}

The chemfig user manual explains this and many other constructions.

But it seems that you are really asking about how to typeset this in MathJax. MathJax is usually considered off topic at TeX.SX. However, the MathJax extension mhchem is also a package in LaTeX, so here is a possible solution using mhchem. It is my understanding that mhchem is designed for chemical equations, not structure diagrams, so you may need to use an array to get this to work:

\documentclass{article}
\usepackage{mhchem}

\begin{document}

\[
\begin{array}{c}
\ce{\phantom{H_3}CH_3}\\% phantom to get the bond aligned with the C
| \\
\ce{CH_3-C-CH_3}\\
| \\
\ce{Cl}
\end{array}
\]

\end{document}

This produces (in LaTeX)

or in Chrome with MathJax:

Related Solutions

[Tex/LaTex] Using the mhchem and chemfig packages in conjunction

Bundling my comments into an answer:

I wrote »There is no way to make chemfigs bonds all the same length. Quoting part II section 4 Length of a bond of chemfig's manual:«

Rather than speaking of length of a bond, we should use the term interatomic spacing. If effect, only the interatomic spacing is adjustable with \setatomsep as we have seen on page 6. Once this parameter is set, the length of a bond depends on the content of atoms and, to a lesser extent, the angle the bond makes with the horizontal. It should be obvious that two “slimmer” atoms will have larger edge separations than two which are larger.

While this was true at the time I wrote my comment meanwhile there has been an update to chemfig. Since version 1.1 the following is possible:

When a star follows the macro \chemfig*, the bonds have a fixed length and therefore, the distance between center to center atoms becomes variable. The macro \enablefixedbondlength makes this behavior valid for all macros (starred or not) while \disablefixedbondlength goes back to the default behavior. [...] In rings, even with starred \chemfig*, the default behaviour is restored in order to draw regular polygons.
Regarding your second point part III section 4 Vertical alignment has some information. It will not be immediately helpful, though, I guess. Nonetheless it is important information. The solution for the formula in your question is simple, though: write your formula in a different way:
```
\chemfig{CH_3-C(=[6]O)-CH3}
```
Keep in mind that the first atom in a formula determines the baseline of the whole formula.
As for your third point I recommend reading the blog post “Exploring ChemFig: Customising appearance” of our own @JosephWright which explains a method of how to use mhchem's \cf inside chemfig's \printatom. The crucial part is a redefinition of \CF@node@content
```
\makeatletter
\def\CF@node@content{%
  \expandafter\expandafter\expandafter
    \printatom\expandafter\expandafter\expandafter
      {\csname atom@\number\CF@cnt@atomnumber\endcsname}%
    \ensuremath{\CF@node@strut}%
}
\makeatother
```
which then allows \renewcommand*{\printatom}[1]{{\sffamily\cf{#1}}} for example.

[Tex/LaTex] How to put chemical formula into subscript with mhchem

Sub- and superscripts should be given in braces if they are not a single token. Whilst some cases do work without this (for example $M_\mathrm{n}$ ) this is not generally true. Here, the document will work correctly with eh official LaTeX syntax

\documentclass{report}
\usepackage[version=4]{mhchem}

\begin{document}
\begin{equation}
    M_{\ce{H}}
\end{equation}

\end{document}

Best Answer

Related Solutions

[Tex/LaTex] Using the mhchem and chemfig packages in conjunction

[Tex/LaTex] How to put chemical formula into subscript with mhchem

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