A new version of Molecules is now available on the App Store, and the available source code has also been updated. The new version fixes a potential crash in iPhone OS 4.0 and adds a new means of directly installing molecular structures in the application.
On the iPad (and soon the iPhone), you can now drag and drop molecular structures into (and out of) Molecules using iTunes. When your device is connected, you can go to the Apps tab and scroll down until the File Sharing section is visible. Within that section, click on Molecules to display all currently loaded molecular structure files. To add a new structure, simply drag it into the list of files. On the next startup of Molecules, it will be parsed and added to the application's internal database.