Dealing with the concepts of “chemical compound” vs. “chemical structure”


Robert S. Pearlman1, Yubin Wu1, Karl M. Smith1, and Brian B. Masek2. (1) Optive Research, Inc, 12331-A Riata Trace Parkway -- Suite 110, Austin, TX 78727, (2) Tripos, Inc, 1699 S. Hanley Rd., St. Louis, MO 63144
Chemical compounds can exist in various protonation states and in various tautomeric states – two aspects of what shall, henceforth, be referred to as the "protomeric state" of a compound. Different protomeric states correspond to different connection tables – hence, different structures – of a compound. A compound’s environment (solvent, membrane, receptor, etc.) determines the protomeric state which the compound is most likely to adopt. Experimentally measured properties reflect Mother Nature’s choice of which structure(s) predominates and determines the measured property value. Regrettably, we often tend to forget these facts when generating or assessing or storing predicted properties of compounds obtained from calculations based on a particular structure we or some other human chose to associate with the compound.

We need to be able to enumerate and consider the various structures which a compound might exhibit in different Natural environments. We need to be able to associate measured data with compounds while associating computed data with the particular structures used for the computations. We need a robust method to associate any given structure with its corresponding, canonically identified compound. This presentation will introduce algorithms and software tools which address these needs and others.