November 23, 2016
by Sherry Myles,
If you have ever booked a flight online, or even Googled how to get to a dream destination, you fully understand the confusion of choosing between multiple itineraries. Will you risk a 45 minute connection in Frankfurt? Settle for an overnight stay in Toronto? Which itinerary is the “best” one for you? Ultimately it doesn’t matter which route you book, you will still arrive at the same destination (and hopefully on the same flight as your luggage).
Similarly, when naming chemical compounds, there are a myriad of correct names that accurately describe the structure. N-methyl-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine, fluoxetine, or Prozac—they can all be interpreted as the same compound. But is there a “more correct” name? There wasn’t, until recently…
In December 2013 the IUPAC “Blue Book” (officially known as the Nomenclature of Organic Chemistry: IUPAC Recommendations and Preferred Names) was published. The long-awaited update to the rules introduced the concept of “Preferred IUPAC Name” (PIN), which defines one preferred name for a compound derived based on strict adherence to the IUPAC naming rules. While PINs are intended for use mainly in regulatory compliance—including compound registrations and patent filings—there are broader effects as well. Compounds such as tetrahydrofuran (or THF) now have a “more correct” name—in this case oxolane. No doubt the THF moniker will stick around, but for hard-to-remember names—the related compound, tetrahydro-2H-pyran, is now known as oxane—the new PIN is a welcome change!
In addition to new rules, new classes of compounds have been introduced in recent years—including fullerenes and cyclophanes—that necessitate the need to update naming practices. The existing, published rules simply didn’t have a method to name these compound classes. As chemistry evolves, so must the practice of naming chemical compounds.
No matter which method you employ to make your travel arrangements (perhaps consulting a web site, or talking to your travel agent), you are ultimately looking for advice on the best itinerary. Similarly with compound naming, there is more than one way to determine the correct name for your structure. Memorizing tedious lists of naming rules may result in the correct name (there is an exhaustive reproduction of the 1993 Blue Book available here); however, unless naming compounds is part of your day-to-day job description, this strategy will consume valuable time and effort and leave uncertainty as to whether you have determined the correct name.
Using a computer program is a much more efficient method and software has naturally taken its place in the lab as an essential tool for naming compounds. While learning naming principles is still important to your education, once you leave the academic environment you will not have to name compounds very often. At this point, accuracy is key. A software program such as ACD/Name, can help you generate the correct name for your structure with confidence and reliability without having to memorize the rules and keep up with changes. How often do you think mistakes happen? A small naming mistake can lead to a very incorrect chemical structure.
You can leave your travel plans to chance, just as you can guess at the best name for a structure. In the same way that you do not want to lose your baggage in Frankfurt, you do not want to publish your research with the wrong chemical name. Software is a reliable way to keep up with new naming rules and principles and has the added benefit of making your nomenclature tasks much easier.