A (perhaps quick and dirty) solution would be to embed each
\chemfig in a
tikzpicture environment for better alignment control.
Code: Select all
\documentclass[11pt]{article}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{geometry}
\usepackage{siunitx}
\usepackage{chemfig}
\begin{document}
\begin{tikzpicture}[baseline=(current bounding box.center)]
\chemfig{N~[7]C-[7](-[7]CH_3)(-[5]CH_3)-[1]N=[7]N-[1](-[1]CH_3)(-[3]CH_3)-[7]C~[7]N}
\end{tikzpicture}
\chemrel[\small\SI{60}{\celsius}]{->}
\begin{tikzpicture}[baseline=(current bounding box.center)]
\chemfig{N~[7]\lewis{0.,C}-[7](-[7]CH_3)(-[5]CH_3)}
\end{tikzpicture}
\chemsign{+}
\begin{tikzpicture}[baseline=(current bounding box.center)]
\chemfig{N~[6]N}
\end{tikzpicture}
\end{document}
I guess alignment depends on the starting point for drawing a molecule. In your case you always started in the upper left corner, thus this is the hook for placing the equations symbols.
Note that the package offers according commands for equation symbols like arrows (see code above). Not related to the problem is the addition of the
siunitx package for physical units.
Best regards and welcome to the board
Thorsten