With rectangular figures you can show more area by placing them vertically: +40% width and staying within the margins,
(Perhaps for looking a SEM does not matter)

\documentclass[14pt]{extarticle}
\usepackage{graphicx, epstopdf}
\usepackage[version=4]{mhchem}
\usepackage{hyperref}
\usepackage{url}
\usepackage[articletitle]{achemso}
\usepackage{amsmath}
\usepackage{gensymb}
\usepackage{fancyhdr}
\usepackage[section]{placeins}
\usepackage{geometry}
\geometry{a4paper,left=3.5cm,top=2.5cm,right=2.5cm,bottom=2.5cm}
\usepackage{subcaption} % added <<<<<<<<<<<<<<<<<<<<<<<<<<<
\usepackage{showframe} % ONLY to show the margins
\begin{document}
\FloatBarrier \section{Scanning electron microscopy}
\begin{figure}[h]
\begin{subfigure}[b]{0.45\linewidth}
\centering
\includegraphics[width=1.4\linewidth, angle=90]{example-image-a} % changed <<<<<<<<<<<<
\caption{Scan I}
\label{fig:scanI}
\end{subfigure}
\qquad
\begin{subfigure}[b]{0.45\linewidth}
\centering
\includegraphics[width=1.4\linewidth,angle=90]{example-image-b} % changed <<<<<<<<<<<<
\caption{scan II}
\label{fig:scanII}
\end{subfigure}
\caption{SEM images of \ce{ZnCr2O4}}
\label{fig:SEM}
\end{figure}
The figure~\ref*{fig:SEM} shows ...
\end{document}
If necessary, the margins can be trespass. (LaTeX will issue a warning)

\documentclass[14pt]{extarticle}
\usepackage{graphicx, epstopdf}
\usepackage[version=4]{mhchem}
\usepackage{hyperref}
\usepackage{url}
\usepackage[articletitle]{achemso}
\usepackage{amsmath}
\usepackage{gensymb}
\usepackage{fancyhdr}
\usepackage[section]{placeins}
\usepackage{geometry}
\geometry{a4paper,left=3.5cm,top=2.5cm,right=2.5cm,bottom=2.5cm}
\usepackage{caption} % captionof <<<<<<<<<<<<<<<
\usepackage{showframe} % ONLY to show the margins
\begin{document}
\FloatBarrier\section{Scanning electron microscopy}
\hspace*{-2cm}\begin{minipage}{1.1\linewidth}
\includegraphics[width=0.55\linewidth]{example-image-a}\quad
\includegraphics[width=0.55\linewidth]{example-image-b}
\captionof{figure}{SEM images of \ce{ZnCr2O4}}
\label{fig:SEM}
\vspace*{\baselineskip}
\end{minipage}
The figure~\ref*{fig:SEM} shows ...
\end{document}
Or mix the two techniques.
Maximum page coverage for comparing two images would be achieved by having one on top of the other.

\noindent\begin{minipage}{\linewidth}
\includegraphics[width=\linewidth]{example-image-a}
\includegraphics[width=\linewidth]{example-image-b}
\captionof{figure}{SEM images of \ce{ZnCr2O4}}
\label{fig:SEM}
\end{minipage}