Preparing Manuscripts

Guidelines

Make sure to read the guidelines for authors for the target journal before starting to write.

Much of our work involves organic synthesis, and we will often submit to J. Org. Chem. And, even if we are submitting elsewhere, the characterization requirements for J. Org. Chem. are excellent and provide a good starting point. Consult their guidelines before starting to prepare your manuscript.

Consult other articles from reliable authors to check on formatting, etc. Here is a paper that I (BTK) like.

To facilitate editing, the manuscript should:

be double spaced
have 1 inch margins
include centered page numbers in the footer

Some Generalities on Writing

read Mastering the Art of Scientific Publishing.

And read the

Organizing all the Files, etc.

Each manuscript will have a single top-level directory on our file server. Subdirectories will include

and other directories as needed.

Formatting and Templates

Initial drafts should be double spaced with 1″ margins and page numbers to facilitate editing and revision. For some journals (e.g. J. Org. Chem.), this format is sufficient for submission. Other journals require the use of specific templates, and, in those cases, the document can be reformatted after the content nears final revisions.

Art

Make sure to read the guidelines for authors for sizes, resolution, font, and other constraints before beginning figures. Here is one article on the preparation of figures. And another.

Filenames and Version Control for Manuscripts

The preparation of a thesis, dissertation, or manuscript for publication involves a generation of many versions of many files.

The best practice is to name files in the format below:

for example, the adobe illustrator version 1-3 (1 major 3 minor) of figure 2 in mypaper saved on 2021 April 2 would be named:

20210402mypaper_figure2_1-3.ai

123456789012345678901234567890 (30 characters)

Use no more than 32 characters. Use only numbers, letters, and underscores. Do not use special characters, dashes, spaces, or multiple dots or stops. Avoid using common terms (‘data’, ‘sample’, ‘final’, or ‘revision’). Use consistent case – all lower case, or all UPPER CASE, or Lower case. Dates should be in a standard format – YYYYMMDD, which will allow them to sort chronologically.

Sequential numbering should allow for growth, and include leading zeros. Do you have 100 files? Numbering should run from 001 to 100.

To convert various document formats, we use pandoc. I’m currently exploring writing in markdown and then converting to doc for final layout.

Referencing

The group uses zotero for referencing, with a shared library. Unless otherwises required by a journal, we will us the ACS + titles, like is used in Accounts of Chemical Research.

Connected papers looks like a nice tool for literature searches.

When preparing bibliographies, make sure that journal abbreviations are in accordance with the CASSI standard.