Chemistry acronym will not integrate correctly in the headline/TOC

Question

I am using \usepackage{acronym} in my nomenclature. However, as I have to include a lot of chemistry in my report, it seems like the preamble setup result in the TOC showing the full acronym, even though the acronym is used in the text before it is used in the headline. So it seems as if the TOC is working separate from the text, which it should not.

\documentclass[a4paper,11pt,fleqn,twoside,openright]{memoir}   
\usepackage[english]{babel}
\usepackage{graphicx}
\usepackage{pdfpages}
\usepackage{multirow}
\usepackage{float}
\usepackage{subcaption}
\usepackage{acronym} 
\usepackage{amsmath,amssymb,stmaryrd}
\usepackage{xfrac}
\usepackage[version=4]{mhchem}
\usepackage{eurosym}
\usepackage[round]{natbib}
\bibliographystyle{0.Litteraturliste/harvard}   
\usepackage{listings}
\usepackage[shortlabels]{enumitem}
\usepackage[colorlinks]{hyperref}
\hypersetup{colorlinks = true,
    linkcolor = black,
    citecolor = black,
    urlcolor = black}
\setsecnumdepth{subsubsection}
\settocdepth{section}
\setlrmarginsandblock{3.5cm}{2.5cm}{*}
\setulmarginsandblock{2.5cm}{3.0cm}{*}
\checkandfixthelayout                   
\setlength{\parindent}{0mm}
\setlength{\parskip}{2mm}
\linespread{1,1}
\captionstyle{\centering}
\captionwidth{\linewidth}
\usepackage{transparent}
\newif\ifchapternonum
\makechapterstyle{jenor}{                   
  \renewcommand\beforechapskip{0pt}
  \renewcommand\printchaptername{}
  \renewcommand\printchapternum{}
  \renewcommand\printchapternonum{\chapternonumtrue}                         \renewcommand\chaptitlefont{\fontfamily{pbk}\fontseries{db}\fontshape{n}\fontsize{20}{30}\selectfont\raggedright}     \renewcommand\chapnumfont{\fontfamily{pbk}\fontseries{m}\fontshape{n}\fontsize{0.7in}{0in}\selectfont\color{black}\transparent{0.6}}
  \renewcommand\printchaptertitle[1]{%
    \noindent
    \ifchapternonum
    \begin{tabularx}{\textwidth}{X}
    {\let\\\newline\chaptitlefont ##1\par} 
    \end{tabularx}
    \par\vskip-2.5mm\hrule
    \else
    \begin{tabularx}{\textwidth}{Xl}
    {\parbox[b]{\linewidth}{\chaptitlefont ##1}} & \raisebox{-15pt}{\chapnumfont \thechapter}
    \end{tabularx}
    \par\vskip2mm\hrule
    \fi
  }
}   
\chapterstyle{jenor}
\makepagestyle{Uni}
\makepsmarks{Uni}{%
    \createmark{chapter}{left}{shownumber}{}{. \ }
    \createmark{subsubsection}{right}{shownumber}{}{. \ }
    \createplainmark{toc}{both}{\contentsname}
    \createplainmark{lof}{both}{\listfigurename}
    \createplainmark{lot}{both}{\listtablename}
    \createplainmark{bib}{both}{\bibname}
    \createplainmark{index}{both}{\indexname}
    \createplainmark{glossary}{both}{\glossaryname}
}
\makeevenhead{Uni}{}{}{\leftmark}
\makeoddhead{Uni}{\rightmark}{}{}
\makeevenfoot{Uni}{\thepage}{}{}
\makeoddfoot{Uni}{}{}{\thepage}
\makeheadrule{Uni}{\textwidth}{0.5pt}
\makefootrule{Uni}{\textwidth}{0.5pt}{1mm}
\copypagestyle{Unichap}{Uni}
\makeoddhead{Unichap}{}{}{}
\makeevenhead{Unichap}{}{}{}
\makeheadrule{Unichap}{\textwidth}{0pt}
\aliaspagestyle{chapter}{Unichap}
\pagestyle{Uni}

\begin{document}
\input{1.Formalia/Titelblad}
\cleardoublepage 
\phantomsection
\pdfbookmark[0]{Indholdsfortegnelse}{indhold}
\tableofcontents*
\addtocontents{toc}{\vskip -0.8cm}
\addtocontents{lof}{\vskip -0.3cm}
\raggedbottom
\cleardoublepage 
\frontmatter
\input{1.Formalia/acro_list}
\mainmatter
\input{2.TEXT/TEXT}
\end{document}

1.Formalia/Titelblad

\phantomsection \thispagestyle{empty} \begin{center} \begin{tabular}{c} {\HUGE\textbf{A nature-based solution to remove}} \ {\HUGE\textbf{hydrogen sulphide}} \end{tabular}
\end{center} \hrulefill \begin{center} \begin{tabular}{lcl} & Master thesis & \
& Department of the Built Environment & \ & Aalborg University & \end{tabular}
\end{center} \textbf{Number of pages} & & XX \ \end{tabular} \begin{center}{\footnotesize\itshape The present report with source references and appendix is not allowed published without prior written approval from either the thesis author, supervisors or external partners. Moreover, the thesis content is not allowed to be employed for commercial purposes without written approval.} \end{center}

1.Formalia/acro_list

\chapter{Nomenclature} \begin{acronym}[MPC] \acro{H_{2}S}[\ce{H_{2}S}]{Hydrogen sulphide} \acro{HS^{-}}[\ce{HS^{-}}]{Bi-sulphide} \acro{S^{2-}}[\ce{S^{2-}}]{Sulphide ion} \acro{SO_{4}^{-2}}[\ce{SO_{4}^{-2}}]{Sulphate} \end{acronym}

2.TEXT/TEXT

\chapter{Towards a sustainable future} Sewers have been found to release greenhouse gases, and some attention has been on the release of \ac{CH_{4}} due to anaerobic processes, however, it seems likely that \ac{N_{2}O} can also be released when \ac{H_{2}S} is managed by addition of \ac{NO_{3}^{-}}. Hence a holistic approach is required where the treatment plant is not seen isolated but as integrated with the treatment plant. This also holds true when addressing why \ac{N_{2}O} emissions vary in a treatment plant, as loadings from the network vary in time, for example in terms of \ac{CH_{4}}, \ac{COD} and flow. \chapter{\ac{H_{2}S} in the sewer system} \ac{H_{2}S} is a pervasive malodorous compound that causes concrete and metal corrosion (Figure \ref{fig:INTROCorrosion}) \citep{Svovlbrintehandbogen, Shypanski2018, JesAsbjornBog, Kiilerich-Kinetics, Zdeb2008, Kiilerich-Precipitation}. A survey from 2016 showed that 39 of the 41 participating Danish water utilities had experienced \ac{H_{2}S}-related issues \citep{DANVAGRUNDFOS}. The presence of \ac{H_{2}S} can be a significant nuisance to the surroundings and cause public dissatisfaction. \cite{DANVAGRUNDFOS} estimated, that the utilities spent an average of six hours per month handling odour complaints with just over half of the utilities having it as a service goal \citep{DANVAGRUNDFOS}. Although the generation of \ac{H_{2}S} can occur in any section of the wastewater conveyance networks, the application of force mains, and the possible anaerobic conditions that follow, are considered to be the main source \citep{Shypanski2018, JesAsbjornBog}. Under anaerobic conditions, \ac{SO_{4}^{-2}} present in the wastewater is reduced to \ac{S^{2-}}, by the \ac{SR} microorganisms residing in the biofilms found on the sewer structure and the sediment, and \ac{H_{2}S} is produced. The build-up of \ac{H_{2}S} in the system is partly released to the surroundings when the wastewater depressurises at the end of the force main (Figure \ref{fig:H2S-Skitse}) \citep{Despot2021, JesAsbjornBog, Kiilerich-Kinetics}. \section{The \ac{S^{2-}} production in the anaerobic biofilm} In sewers, biofilms are an extracellular matrix, consisting of polymeric substances excreted by the microorganisms living within it, adhering to the submerged inner surface of the sewer wall and the bottom sediment \citep{OxyChem, Shiba, JesAsbjornBog, Despot2021, Victoria2021}. Biofilm can also be found on moist surface areas, such as areas that are exposed to the water phase, resulting either from capillary forces or condensation of the high humidity in the sewer air \citep{JesAsbjornBog}. The gelatinous biofilm can be compartmentalised into different zones depending on the presence and concentration of electron acceptors \citep{JesAsbjornBog, ZHANG20081, Svovlbrintehandbogen}.

Hope you can help me fix this :-)

---

When using \ac*{} in all the headline instead of \ac{}, the following happen:

---

When adding the following changes in the preamble:

\usepackage[version=4]{mhchem}
\mhchemoptions{font=sf}

The \Ac{} and \ac{} string does not produce the expanded acronym with the acronym in brackets, when the acronym is first utilised, as shown on the picture.

I do not know If this is because I have a list of tables and a list of figures before the actual text, which makes the caption the first acronym appearance or if the chapter headline function as the first appearance.

Draft document with the necessary information about the document setup.

Answer 1

Well, at first mhchem and acronym threw some obscure errors at me using your samples. But then the mhchem manual gave the clue to solve that. So this is the resulting MWE that offers a solution to your question:

\documentclass[11pt]{report}

\usepackage[a4paper,margin=2cm]{geometry}

\usepackage[version=4]{mhchem}
    \mhchemoptions{font=sf}
    
\usepackage{acronym}

\begin{document}
    
    \tableofcontents
    
\chapter{\Acl{H2S} in the sewer system}

     \Ac{H2S} is a pervasive malodorous compound that causes concrete and metal corrosion (Figure A) . A survey from 2016 showed that 39 of the 41 participating Danish water utilities had experienced \ac{H2S}-related issues. The presence of \ac{H2S} can be a significant nuisance to the surroundings and cause public dissatisfaction.  estimated, that the utilities spent an average of six hours per month handling odour complaints with just over half of the utilities having it as a service goal .   

    Although the generation of \ac{H2S} can occur in any section of the wastewater conveyance networks, the application of force mains, and the possible anaerobic conditions that follow, are considered to be the main source. Under anaerobic conditions, \ac{SO42-} present in the wastewater is reduced to \ac{S2-}, by the \ac{SR} microorganisms residing in the biofilms found on the sewer structure and the sediment, and \ac{H2S} is produced. The build-up of \ac{H2S} in the system is partly released to the surroundings when the wastewater depressurises at the end of the force main (Figure B).

\section{The \acs{S2-} ion production in the anaerobic biofilm}
    
    In sewers, biofilms are an extracellular matrix, consisting of polymeric substances excreted by the microorganisms living within it, adhering to the submerged inner surface of the sewer wall and the bottom sediment . Biofilm can also be found on moist surface areas, such as areas that are exposed to the water phase, resulting either from capillary forces or condensation of the high humidity in the sewer air . The gelatinous biofilm can be compartmentalised into different zones depending on the presence and concentration of electron acceptors.

\section{Acronyms}
    
    \begin{acronym}[H2CO3]
        \acro{H2CO3}[\ce{H2CO3}]{carboxylic acid}
        \acro{H2S}[\ce{H2S}]{dihydrogen sulfide}
        \acro{S2-}[\ce{S^{2-}}]{sulfide ion}
        \acro{H+}[\ce{H+}]{hydrogonium ion}
        \acro{SO42-}[\ce{SO_{4}^{2-}}]{sulfate ion}
        \acro{SR}{sulfonamide resistant}
    \end{acronym}
    
\end{document}

This MWE gives the following toc as result:

Depending whether you want the full name of the compound in the chapter / section you use \acl{} (or \Acl{} at the start of a sentence) or \acs{} for the formula of that compound.

Note you may need to adapt the way you entered your acronyms. The use math related notations in the acronym names threw errors about missing $ among others. The acronym manual shows the proper use (and the reason why) on page 4. Replacing your acronyms with the ones I suggest can be simply done in any editor using the Search and Replace functionality.

Edit The OP provided a sample in Overleaf to work with. After altering the \ac{abbr}to either \acl{abbr} or \acs{abbr} the toc looked correctly:

Intext the use of \acf{abbr} may be required to insert the full name plus acronym in parentheses.

Answer 2

This is the complete fix, that the @alchemist provided in the draft Overleaf document.

\documentclass[a4paper,11pt,fleqn,twoside,openright]{memoir}
\usepackage[english]{babel}
\usepackage{graphicx}
\usepackage{pdfpages}
\usepackage{multirow}
\usepackage{float} 
\usepackage{subcaption}
\usepackage{acronym} 
\usepackage[version=4]{mhchem}
   \mhchemoptions{font=sf}
\usepackage{xfrac}
\usepackage{amsmath,amssymb,stmaryrd}
\usepackage{eurosym}
\usepackage{listings}
\usepackage[shortlabels]{enumitem}
\usepackage{transparent}
\newif\ifchapternonum
\makechapterstyle{jenor}{                   
   \renewcommand\beforechapskip{0pt}
   \renewcommand\printchaptername{}
   \renewcommand\printchapternum{}
   \renewcommand\printchapternonum{\chapternonumtrue}
   \renewcommand\chaptitlefont{\fontfamily{pbk}
   \fontseries{db}\fontshape{n}
   \fontsize{20}{30}\selectfont\raggedright}
   \renewcommand\chapnumfont{\fontfamily{pbk}
   \fontseries{m}\fontshape{n}\fontsize{0.7in}{0in}\selectfont\color{black}\transparent{0.6}}
   \renewcommand\printchaptertitle[1]{
   \noindent
   \ifchapternonum
   \begin{tabularx}{\textwidth}{X}
    {\let\\\newline\chaptitlefont ##1\par} 
   \end{tabularx}
   \par\vskip-2.5mm\hrule
   \else
   \begin{tabularx}{\textwidth}{Xl}
{\parbox[b]{\linewidth}{\chaptitlefont ##1}} & \raisebox{-15pt}{\chapnumfont \thechapter}
\end{tabularx}
\par\vskip2mm\hrule
\fi
 }
 }  
 \chapterstyle{jenor}   
\makepagestyle{Uni}
\makepsmarks{Uni}{
\createmark{chapter}{left}{shownumber}{}{. \ }
\createmark{subsubsection}{right}{shownumber}{}{. \ }
\createplainmark{toc}{both}{\contentsname}
\createplainmark{lof}{both}{\listfigurename}
\createplainmark{lot}{both}{\listtablename}
\createplainmark{bib}{both}{\bibname}
\createplainmark{index}{both}{\indexname}
\createplainmark{glossary}{both}{\glossaryname}
 }
 \makeevenhead{Uni}{}{}{\leftmark}
 \makeoddhead{Uni}{\rightmark}{}{} 
 \makeevenfoot{Uni}{\thepage}{}{}
 \makeoddfoot{Uni}{}{}{\thepage}
 \makeheadrule{Uni}{\textwidth}{0.5pt} 
 \makefootrule{Uni}{\textwidth}{0.5pt}{1mm} 
 \copypagestyle{Unichap}{Uni}
 \makeoddhead{Unichap}{}{}{}
 \makeevenhead{Unichap}{}{}{}
 \makeheadrule{Unichap}{\textwidth}{0pt}
 \aliaspagestyle{chapter}{Unichap}   
 \pagestyle{Uni}

 \begin{document}
 \phantomsection
 \thispagestyle{empty}
 \begin{center}
 \begin{tabular}{c}
  {\HUGE\textbf{A nature-based solution to remove}}
  \\
  {\HUGE\textbf{hydrogen sulphide}}
\end{tabular}  
\end{center}
\hrulefill
\begin{center}
\begin{tabular}{lcl}
& Master thesis &
\\  
& Department of the Built Environment &
 \\
& Aalborg University &
\end{tabular}  
\end{center}
\begin{center}{\footnotesize\itshape The present report with source references and appendix is not allowed published without prior written approval from either the thesis author, supervisors or external partners. Moreover, the thesis content is not allowed to be employed for commercial purposes without written approval.}
\end{center}
\cleardoublepage 
\phantomsection 
\tableofcontents*
\addtocontents{toc}{\vskip -0.8cm}
\addtocontents{lof}{\vskip -0.3cm}
\raggedbottom
\cleardoublepage 
\frontmatter

\begin{acronym}[Sulfilogger]
\acro{H2S}[\ce{H_{2}S}]{hydrogen sulphide}
\acro{HS-}[\ce{HS^{-}}]{bi-sulphide ion}
\acro{S2-}[\ce{S^{2-}}]{sulphide ion}
\acro{SO42-}[\ce{SO_{4}^{2-}}]{sulphate ion}
\acro{H2SO4}[\ce{H_{2}SO_{4}}]{sulphuric acid}
\acro{H+}[\ce{H^{+}}]{hydrogen ion}
\acro{pH-meter}{pH 3110 from WTW\textsuperscript{TM}}
\acro{alpha}[\ensuremath{\alpha}]{conversion coefficient}
\acro{Sulfilogger}{SulfiLogger\textsuperscript{TM} S1/X1-1020 from SulfiLogger A/S (Aarhus, Denmark)}
\acro{Odalog}{OdaLog\textregistered L2 Gas Logger from Thermo Fisher Scientific Inc}
\acro{SR}{Sulphate-reducing}
\end{acronym}

\cleardoublepage
\listoffigures
\cleardoublepage

\mainmatter
\chapter{\Acl{H2S} in the sewer system}
\Acf{H2S} is a pervasive malodorous compound that causes concrete and metal corrosion (Figure \ref{fig:INTROCorrosion}). A survey from 2016 showed that 39 of the 41 participating Danish water utilities had experienced \ac{H2S}-related issues. The presence of \ac{H2S} can be a significant nuisance to the surroundings and cause public dissatisfaction. DANVAGRUNDFOS estimated, that the utilities spent an average of six hours per month handling odour complaints with just over half of the utilities having it as a service goal. 
\begin{figure}[H]
\centering
\includegraphics[width=0.7\textwidth]{Korodering2.JPG}
\caption{Concrete structure at Tranbjerg pumping station with a sprayed-on pH indicator, which visualises the alkalinity through the appearance of colours with blue colours representing alkaline conditions and red colours representing acidic conditions. The presence of the red colours on the concrete structure indicates the adsorption of \ac{H2S} gas onto the damp surfaces of the structure material and the subsequent oxidation of the \ac{H2S} into the acidic \ac{H2SO4}. Photo taken by Asbjørn Haaning Nielsen.}
\label{fig:INTROCorrosion}
 \end{figure}

 \section{The \acs{S2-} production in the anaerobic biofilm} 
 \acf{SR} microorganisms, primarily \textit{Desulfovibrio} and \textit{Desulfotomaculum}, will subsequently oxidise the readily biodegradable organic substrate and, during the process, reduce the commonly found \ac{SO42-} to \ac{S2-}. 

 \section{Release of \acl{H2S} into the sewer atmosphere}
 When the \ac{S2-} diffuses into the liquid phase from the biofilm, it combines with the available \ac{H+} and dissociates into total dissolved \acl{S2-}, which is the pH-dependent mixture of \ac{HS-}, \ac{H2S} and \ac{S2-}. Bla... \ac{alpha}
 \end{document}