You can find more tips on how to write a compelling M.S. thesis using the Gredig Lab Guidelines. If the Bibliography file needs to be shortened, then use LaTeX Trim BibTeX Utility. You should cite other M.S. thesis work, whenever you are using their work. Here is an automated way to generate the bibliography items, using the ProQuest Citation Generator.

First, clone the M.S. Thesis Template.

Using the ChemFig package in LaTeX, you can generate the Phthalocyanine molecule as follows:

 

\begin{figure}[H] \subfigure[\ch{C6H4(CN)2}]{
\scriptsize
\chemfig{*6(-=(-CN)-(-CN)=-=)} % phthalonitrile
}
\subfigure[\ch{CuC32N8H16}]{
\scriptsize
\chemfig{N?(=[::+72]*5(-N-(=N-[::-72]*5(=[,,,1]N-[,,1](=N-[::-36]*5(-N-(-N=[::-72]*5(-N=[,,1]?-*6(-=-=-=)–))=*6(-=-=–)-=))-*6(-=-=–)=-))-*6(-=-=-=)–))-[,,,,draw=none]-[,,,,draw=none]Cu(-[:55,,,,dash pattern=on 2pt off 1pt])(-[:-55])(-[:125])(-[:-125,,,,dash pattern=on 2pt off 1pt])}
}
\caption{The phthalonitrile in (a) is used to make copper phthalocyanine in (b).}
\end{figure}

Here is the output of this figure:

ChemFig with Phthalocyanine Molecule

If the box is overfull and LaTeX document goes into the edge space, then enable sloppy mode, as in:

\begin{sloppypar} % avoid paragraph being too long and spill over next line.
This text is very narrow and has a long number in math mode, \SI{12.4132 x 9875.232}{\nano\meter}.
\end{sloppypar}

BibTeX has several entries like @masterthesis and @article as well as several fields. The Type has to be defined for mastersthesis, otherwise, it will say "Unpublished Master's Thesis", when using APA style

\bibliographystyle{apacite}

This is also discussed in the MSthesis-ProQuest-Cite Repository.