Create a simple "scheme" environment and a "List of Schemes"
Here is how you can combine chemmacros' scheme module with subcaption and cleveref.
- List of Schemes:
- References to schemes and subschemes:
- Captions of schemes:
\documentclass[oneside,11pt]{book}
\usepackage[semibold,tt=false]{libertine}
\usepackage{libertinust1math}
\usepackage[font={sf,small},labelsep=quad,labelfont=sc]{caption}
\usepackage[subrefformat=parens]{subcaption}
\usepackage[
expansion = false ,
tracking = smallcaps ,
letterspace = 40 ,
]{microtype}
\usepackage{booktabs}
\usepackage{acro}
\acsetup{
barriers/use, barriers/reset,
use-id-as-short,
}
\newcommand{\ie}{i.e.}
\newcommand{\eg}{e.g.}
\newcommand{\cf}{cf.}
\newcommand{\avg}[1]{\overline{#1}}
\usepackage{mdframed}
\usepackage{chemformula}
\setchemformula{charge-hshift=.5pt}
\usepackage{chemmacros}
\chemsetup{modules=scheme}
\AtEndPreamble{\DeclareCaptionSubType*{scheme}}
\usepackage{graphicx}
\usepackage{enumitem}
\usepackage{calc}
\usepackage{tabto}
\usepackage[titles]{tocloft}
\setlength{\cftfignumwidth}{2.9em}
\setlength{\cfttabnumwidth}{2.9em}
\usepackage[capitalize]{cleveref}
\crefformat{subscheme}{\schemename~#2#1#3}
\begin{document}
\addcontentsline{toc}{chapter}{\listfigurename}
\listoffigures
% \phantomsection %% Remove if using hyperref
\addcontentsline{toc}{chapter}{\listtablename}
\listoftables
\addcontentsline{toc}{chapter}{\listschemename}
\listofschemes
\chapter{First chapter}
Text in the first chapter.
Refer to \cref{fig:firstfig} using cleveref package.
Refer to \cref{tbl:firsttbl}.
Refer to \cref{fig:multi}, \cref{fig:multi:a}, and \cref{fig:multi:b}.
Refer to eventual scheme, \cref{scm:eventualscheme}.
Refer to eventual multi-part scheme, \cref{scm:eventualmultischeme}, \cref{scm:eventualmultischeme:a}, and \cref{scm:eventualmultischeme:b}.
\begin{figure}[!h]
\caption{Caption of figure in first chapter.}\label{fig:firstfig}
\end{figure}
\begin{table}[!h]
\caption{Caption of table in first chapter.}\label{tbl:firsttbl}
\end{table}
\begin{figure}[!h]
\begin{subfigure}{\textwidth}
\phantomsubcaption\label{fig:multi:a}
\end{subfigure}
\begin{subfigure}{0pt}
\phantomsubcaption\label{fig:multi:b}
\end{subfigure}
\caption{Caption of figure referring to parts \subref{fig:multi:a} and \subref{fig:multi:b} with subref command.}\label{fig:multi}
\end{figure}
\begin{scheme}[!h]
\caption{Caption of scheme.}\label{scm:eventualscheme}
\end{scheme}
\begin{scheme}[!h]
\begin{subfigure}{\textwidth}
\phantomsubcaption\label{scm:eventualmultischeme:a}
\end{subfigure}
\begin{subfigure}{0pt}
\phantomsubcaption\label{scm:eventualmultischeme:b}
\end{subfigure}
\caption{Caption of scheme referring to parts \subref{fig:multi:a} and \subref{fig:multi:b} with subref command.}\label{scm:eventualmultischeme}
\end{scheme}
\chapter{Second chapter}
Text in the second chapter.
Refer to \cref{fig:secondfig}.
\begin{figure}[!h]
\caption{Caption of figure in second chapter.}\label{fig:secondfig}
\end{figure}
\begin{scheme}[!h]
\caption{Caption of scheme.}\label{scm:eventualscheme2}
\end{scheme}
\end{document}
Side note: Prior to version 5.11a (2020-11-21) chemmacros \listofschemes was incompatible with the book class. (See also: corresponding bug report) If the above solution does not work for you, consider updating to version 5.11a or newer.
To keep this answer short, I have removed the MWE that used version 5.11 and in which I showed how to overcome some formatting inconsistencies between the list of schemes and the list of figures.
Load the newfloat package and the scheme module for chemmacros.
You just have to set up a subscheme environment for subcaption, which has to be done at begin document.
I loaded tocbibind for adding \listoffigures and \listoftables to the table of contents. Your manual method is incorrect: you should at least have \cleardoublepage before \addcontentsline.
\documentclass[oneside,11pt]{book}
\usepackage[semibold,tt=false]{libertine}
\usepackage{libertinust1math}
\usepackage[font={sf,small},labelsep=quad,labelfont=sc]{caption}
\usepackage[subrefformat=parens]{subcaption}
\usepackage{newfloat}
\usepackage[
expansion = false ,
tracking = smallcaps ,
letterspace = 40 ,
]{microtype}
\usepackage{booktabs}
\usepackage{acro}
\usepackage{mdframed}
\usepackage{chemformula}
\usepackage{chemmacros}
\usepackage{graphicx}
\usepackage{enumitem}
\usepackage{calc}
\usepackage{tabto}
\usepackage[titles]{tocloft}
\usepackage[nottoc]{tocbibind}
\usepackage[capitalize]{cleveref} % should be last
% acro options
\acsetup{
barriers/use, barriers/reset,
use-id-as-short,
}
% chemmacros options
\usechemmodule{scheme}
% chemformula options
\setchemformula{charge-hshift=.5pt}
% tocloft options
\setlength{\cftfignumwidth}{2.9em}
\setlength{\cfttabnumwidth}{2.9em}
% caption options
\AtBeginDocument{\DeclareCaptionSubType*[alph]{scheme}}
% personal commands
\newcommand{\ie}{i.e.}
\newcommand{\eg}{e.g.}
\newcommand{\cf}{cf.}
\newcommand{\avg}[1]{\overline{#1}}
\begin{document}
\tableofcontents
\listoffigures
\listoftables
\listofschemes
\chapter{First chapter}
Text in the first chapter.
Refer to \cref{fig:firstfig} using cleveref package.
Refer to \cref{tbl:firsttbl}.
Refer to \cref{fig:multi}, \cref{fig:multi:a}, and \cref{fig:multi:b}.
Refer to eventual scheme, \cref{scm:eventualscheme}.
Refer to eventual multi-part scheme, \cref{scm:eventualmultischeme}.
% Example figure
\begin{figure}[!h]
\centering
\includegraphics[width=0.02\textwidth]{example-image}
\caption{Caption of figure in first chapter.}\label{fig:firstfig}
\end{figure}
% Example table
\begin{table}[!h]
\centering
\begin{tabular}{ll}
\toprule
A & B\\
\bottomrule
\end{tabular}
\caption{Caption of table in first chapter.}\label{tbl:firsttbl}
\end{table}
% MULTIPART FIGURE
\begin{figure}[!h]
\centering
\begin{subfigure}{0.45\textwidth}
\centering
\includegraphics[width=0.02\textwidth]{example-image}
\phantomsubcaption\label{fig:multi:a}
\end{subfigure}
\begin{subfigure}{0.45\textwidth}
\includegraphics[width=0.02\textwidth]{example-image}
\phantomsubcaption\label{fig:multi:b}
\end{subfigure}
\caption{Caption of figure referring to parts \subref{fig:multi:a} and \subref{fig:multi:b} with subref command.}\label{fig:multi}
\end{figure}
\begin{scheme}[!h]
\centering
\includegraphics[width=0.02\textwidth]{example-image-a}
\caption{Caption of eventual scheme.}\label{scm:eventualscheme}
\end{scheme}
\begin{scheme}[!h]
\centering
\begin{subscheme}{0.45\textwidth}
\centering
\includegraphics[width=0.02\textwidth]{example-image-a}
\phantomsubcaption\label{scm:eventualmultischeme:a}
\end{subscheme}
\begin{subscheme}{0.45\textwidth}
\includegraphics[width=0.02\textwidth]{example-image-b}
\phantomsubcaption\label{scm:eventualmultischeme:b}
\end{subscheme}
\caption{Caption of eventual scheme referring to parts \subref{fig:multi:a} and \subref{fig:multi:b} with subref command.}\label{scm:eventualmultischeme}
\end{scheme}
\chapter{Second chapter}
Text in the second chapter.
Refer to \cref{fig:secondfig}.
% Another example figure
\begin{figure}[!h]
\centering
\includegraphics[width=0.02\textwidth]{example-image}
\caption{Caption of figure in second chapter.}\label{fig:secondfig}
\end{figure}
\end{document}
As @leandriis noted in the comments, the chemmacros package apparently already does what you want.
Otherwise, you just have to add the lines
\usepackage{newfloat}
\DeclareFloatingEnvironment[fileext=los,placement={!ht},name=Scheme]{myscheme}
\captionsetup[myscheme]{labelfont=bf}
\crefname{myscheme}{scheme}{schemes}
to your preamble and then can use a new float type myscheme similar to figures. The list of schemes is produces with \listofmyschemes.