mhchem
I'm using mhchem for chemical formulas. In the body of the text it is fine, but it is given me nasty outputs for the titles on the index of my pdf reader. I have tried different ones and the result comes to be the same. Instead of \ce{IrO2} it appears 3222378.
Has someone encountered a similar problem?
Your code isn't working as it stands:
the second line is not in math mode or inside \ce so _ must issue an error.
Li_{2}(SO_{4})_{0.5}
In the third and fourth line the groups are not balenced but miss a }. After correcting this:
\begin{equation} X_{\ce{Li2(SO4)0.5}} \end{equation}
\begin{equation} X_{\ce{Li2(SO4)_{0.5}}} \end{equation}
the behaviour of the third is documented mhchem behaviour to display adducts so the forth is not a workaround but the way to go.
\documentclass{article}
\usepackage[version=3]{mhchem}
\begin{document}
\ce{Li2(SO4)_{0.5}}
Adduct: \ce{Na2SO4.10H2O}
\begin{equation}
X_{\ce{Li2(SO4)_{0.5}}}
\end{equation}
\end{document}
Alternatively one can use (my own) chemformula:
\documentclass{article}
\usepackage{chemformula}
\begin{document}
\ch{Li2(SO4)_{0.5}}
Adduct: \ch{Na2SO4 * 10 H2O}
\begin{equation}
X_{\ch{Li2(SO4)_{0.5}}}
\end{equation}
\end{document}
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\enablefixedbondlengthmakes this behavior valid for all macros (starred or not) while\disablefixedbondlengthgoes 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.
Best Answer
The problem is that bookmarks can't handle things like math, colors, or font changes. You can use
\texorpdfstring; the first argument will be used in the document and the second one will be used in the bookmarks: