This is the template I modified for my PhD thesis. It does everything natively including organic molecule structures, compound numbering and referencing.
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The package uses mchem and chemfig to write chemical equations, draw organic structures and to follow compounds with compound numbers.
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Use LuaLaTeX to generate the pdf output.
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Checkout the LaTeX/Chapters/Example.tex to see how to add schemes, drawings and reference in text.
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Change variables in the Thesis.cls file and comment out the example files.
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There are also Experimental templates which make compound entries look rather nice with copy and paste assignments for NMR spectra.
Please let me know if you have any issues.