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Do you have the 2.0 OS update for the iPod Touch installed? I know that came out later yesterday and some people had trouble getting it to install.
If so, connect your iPod Touch and to to the "Applications" folder. "Sync Applications" should be checked. If the "All Applications" radio button is not selected, make sure that Molecules has a checkmark next to it in the "Selected Applications" lists.
If all that is correct, make sure that the icon for Molecules didn't end up on the second or third pages of applications on your iPod. Sometimes the new applications end up being added to a later page.