Most papers that include molecular models publish the atomic coordinates and total energies in the supporting information. The list of coordinates can be easily downloaded, saved on your computer, and converted into a Spartan’14 model by following these steps:

• Download the supporting information to your computer

Go to the journal article’s download page. Follow the link to the Supporting Info and save the PDF file to your computer. Example: at dx.doi.org/10.1021/ol061085x there is a link to ol061085xsi20060607_101706.pdf (97 KB).

• Open the PDF file. Locate the coordinates. Select and copy these into another file. Save the latter file as text.

Continuing with our example, the model numbers of the transition states that appear in the paper are also listed in the supporting information. The coordinates for the model follow the model number. Find a model of interest and select just the lines of text that contain atom labels + atomic coordinates. Copy these lines of text (and only these lines) into an empty file and save them as text. (Windows users: Notepad and Wordpad are good programs for creating text files, but they will set the file extension to “.txt” which will need to be fixed in the next step.)

• Rename the text file so that it has the extension “.xyz”

If your computer is hiding the file extensions, tell it to stop that and show you the extensions. The file you saved in the previous step might have been named, “ts7.txt”, and it should be renamed “ts7.xyz” after this step.

• If necessary, move the text file to the computer where you plan to use Spartan’14

• Open the .xyz file from Spartan’14

Open Spartan’14. Select File: Open. By default, the file browser window shows only Spartan Doc’s (*.spartan) files so change that menu to read All Files (*) (*.*). Find your .xyz file, select it, click Open, and voilá.

• Check your model carefully. Then save it as a .spartan file

You will only see the atoms that you copied from the supporting information into the text file. If you slipped up and overlooked an atom, they won’t appear in the Spartan model. Check carefully.

Also, this model just contains the atomic (nuclear) coordinates. If you want to obtain its energy or electronic structure, select Setup: Calculations and calculate the model’s Energy using either the authors’ computational method (this should give results identical to what was published) or whatever method you find convenient.