Obsidian is not handling long equations very well by default. What you can do is adding a snippet to make the long equations scroll horizontally:
/* Scrolling long equations */
.math-block {
padding: 0px;
overflow-x: auto;
}
Together with the plugin “Hider” you can hide the scrollbars.
Secondly it is a good practice to break long equations with for example {aligned} or {gathered}. I don’t know how to do it properly with chemical equations, but here is an example:
$$
\begin{aligned}
& \text{Word A} \xrightarrow{\text{Some text to make a long arrow}} \\
& \qquad \text{Word A} \xrightarrow{\text{Some text to make a long arrow}} \\
& \qquad \qquad \text{Word A} \xrightarrow{\text{Some text to make a long arrow}} \\
& \qquad \qquad \qquad \text{Word A} \xrightarrow{\text{Some text to make a long arrow}}
\end{aligned}
$$
