Paper #4 – Importing published models into Spartan

Authors often file additional material with their papers that does not get published in the journal proper. This material is referred to as supporting (or supplementary) information and often contains important additions to the basic paper.

For example, the experiment-based papers that appear in a rapid-publication journal like Organic Letters usually contain only summaries of the research. Detailed experimental procedures, spectroscopic data, and crystallographic data, are published on-line as supplements.

Nearly all journals expect computational chemists to provide supporting information for their papers. At the very least, the chemist is expected to provide lists of the atomic Cartesian coordinates for each model, but other model properties may be demanded too.

A coordinate list can serve two purpose. First, it makes it possible for another scientist to repeat the calculation and check it for errors. Also, and from our point of view more important, a coordinate list can be converted into a “3-D” model so we don’t have to rely solely on the small flat figures in the journal to see what is going on.

You can use Spartan to view published models if you know how to convert the data in the supporting info into a file format that Spartan recognizes. The conversion procedure that I followed for paper #4 can be briefly summarized as:

1. Download & open supporting information
2. Copy atom coordinates to clipboard
3. Paste atom coordinates into a text file
4. Save text file with .xyz extension
5. Open file in Spartan