Latex macro using a specific character (") in bookdown

I have the following latex macro that I used in previous projects to add new terms to the margins of the document:

\newcommand{\margintext}[1]{\setstretch{0.4}    \raggedright{\tiny{\textsf{\uppercase{#1}}}}}

\catcode`\"=13  % make the double quote character " active
\gdef"#1"{\textit{#1}\marginpar{\margintext{#1}}\index{#1}}

\newcommand{\new}[2]
{\textit{#2}\marginpar{\margintext{#1}}\index{#1}}

The idea is that wherever I use quotation marks the function will be invoked. I am now writing my thesis in bookdown and want to use this macro. I import it in the following way:

output:
  thesisdown::thesis_pdf: 
    includes:
      in_header: define_terms.tex

But this doesn't work. Calling the function new from within the document works, but quotation marks are completely ignored.

Any advice?

Thanks!