Chemistry 324 - Spring 2008

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

In greater detail, the procedure goes like this:

Step #1 - Download & open supporting information

Supplements are usually available on-line at the same URL as the paper. In general, hunt around the paper’s web page looking for a link to the supplement.

In the case of paper #4, suppose you had started by using the DOI code (10.1021/ol061085x) to navigate to the paper’s URL, i.e., you had typed http://dx.doi.org/10.1021/ol061085x. The paper URL contains a set of buttons on the right side of the window. Press the button that links to the Supporting Info.

On the next web page, scroll down to the list of Available Supporting Information and download the PDF file to your computer.

Open the PDF file Foxit Reader (or Acrobat Reader, or any PDF reader that allows you to select text). Notice that the file contains information about several models.

Step #2 - Copy atom coordinates to clipboard

A portion of the data page for transition state 7 is shown below as it appears in the Foxit PDF Reader. I have selected coordinates for the first four atoms, but I really will select the coordinates of all atoms.

By the way, notice that each atom’s data requires one line and consists of four items: atom label, x coordinate, y coordinate, and z coordinate. Select the entire line. Select all of the lines of atom data (but do not select anything else), and copy them to the clipboard.

The header in the image states that the coordinates are given in Angstroms. Spartan expects this, so no additional effort is required. However, if the authors had printed the coordinates in atomic units (Bohr), you would need to convert them into Angstroms before you could import them into Spartan.

Step #3 - Paste atom coordinates into a text file

On a Windows PC, open the Notepad program (usually hidden under Start: All Programs: Accessories) and paste the clipboard’s contents into a new file. Don’t worry about the spacing of the data. You don’t have to make things look pretty.

Step #4 - Save text file with .xyz extension
Notepad’s default extension is .txt. Spartan won’t recognize a text file. Select File: Save As and save the file with .xyz as the extension instead.

Step #5 - Open file in Spartan

Start Spartan and select File: Open. Spartan looks for .spartan and .spinput files by default so change the Files of type menu (located at the bottom of the Open window) to read All Files. Find your .xyz file and voilá.