You cite a couple of issues, I'm assuming that this means that the PR is not yet ready to review/merge. Let me know when these issues have been resolved and I'll review.

Regarding the three issues you mentioned:

1. Does an email address have to be a hyperlink? (i.e. is this an official rule from ACS?) If not, I'd say just leave it alone. I do not think it is a super important issue.
2. What is the native LaTeX syntax to write multiple authors using the achemso package?
3. No big deal. If ACS publications customize LaTeX environments/commands so heavily, we do not have to use native Markdown. My only concern is the R code chunks and their output. I'm not sure if the default output satisfy the publication requirement of ACS. I think you will need to give one or two examples on this. Without R code chunks in R Markdown documents, it does not make much sense using R Markdown at all (you can always write a pure LaTeX document).

I have solved the second issue and add R code chunks in the text in a new push. So the only issue is the email.
In ACS publications, the address should not to be a hyperlink. However, without the hyperref package, the email address will be shown as follows in the tex file:

\email{\href{mailto:[email protected]}{[email protected]}}

When complied, the final pdf will show as plain tex.

However, when I add the hyperref package, the compiling totally failed and I think this issue due to some wired definition of \email in the achemso package.

Another way is just removing the \href{mailto:[email protected]} to make the email part look like the following code:

\email{[email protected]}

This make the compile passed. So I think the easiest way is remove some parameters from pandoc to let markdown not convert email address into a hyperlink mode automatically. However, it seemed I can only add parameter instead of removing them in Rmarkdown and I need some help here.

You may test the email issue in the following code:

devtools::install_github('yufree/rticles')

Thank you!

I think I have found the solution. When I remove the --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash from the pandoc command(in fact, just remove +autolink_bare_uris will help), the output will be fine. But it seemed that this command was added to any knit command and I have no idea about how to remove this parameter from the default command. Maybe some optional from Rstudio will fix this issue.

Does it work if you do not use the \email{} command at all?

I tried, but it failed. It seemed the achemso package has a strict definition about \email to make sure the email show at a proper position. This package even contain no \maketitle to show the title and author in the tex file.

Fair enough. That is why I sometimes really hate LaTeX...

This particular problem is not too difficult to solve, though. You just use raw commands \email{} in R Markdown. I have fixed it and merged the PR. Thanks!

Thank you very much! Finally I could write my paper in Rstudio. If I submit to another publication, I'd like to make such template for this package.

P.S.: achemso package template could deal with about 40+ journals for rticles package.

Cool. Please feel free to improve the existing template or contribute new ones. Thanks!