Atomic mass changes in PubChem

PubChem is now using the latest International Union of Pure and Applied Chemistry (IUPAC) recommendations for atomic mass and isotopic composition information.  In addition, PubChem is now restricting the allowed isotopes for a given element to those with a half-life of one millisecond or greater.

Fundamental changes within atomic mass information

Hydrogen and DeuteriumNormally atomic mass updates are not blog worthy; however, there are some fundamental changes in the way masses are conceptualized that affect the atomic weight values computed for nearly all compounds in PubChem.

Molecular weight is one of the most frequently requested pieces of information about a chemical.  To compute a molecular weight of a molecule, one consults a periodic chart and sums the average atomic weights of the elements comprising the chemical, while considering any specified isotopic enrichment information.  Although the molecular weight computation seems straightforward, as greater degrees of precision in atomic masses are known, the chemical science community is recognizing complex issues with average atomic weight and isotopic data.

The abundance ratio between different isotopes of a given element is used to determine its average atomic weight.  As the sensitivity of measuring equipment has increased, scientists now notice a distinct difference in these abundance ratios depending on the material source of that element.  To reflect this variation, and as explained in this IUPAC technical report, many elements are now given an atomic weight interval, consisting of a range of known discrete values reflecting the varying isotopic abundance ratios found in different elemental material sources. For example, the atomic weight interval of carbon is 12.0096 to 12.0116.

Another complicating factor is that the abundance ratio of naturally occurring isotopes is not available for all elements.  Some elements like radon do not have any stable isotope and no characteristic isotopic composition in earthly materials.  It means that no average atomic weight can be determined!  There are also a growing number of elements that do not exist in nature, being “synthesized” in the lab.  These artificially created elements are metastable, rapidly decaying into other elements.  Importantly, because different isotopes of a given element decay at different rates, the isotopic abundance ratio between isotopes is time-dependent.

All of these considerations contribute to the uncertainty in atomic weight and isotopic information, which in turn impacts the molecular weight of a compound.

What changes did PubChem make?

All molecular weights in the PubChem Compound database were updated as such:

  • Adoption of “conventional atomic weights”Periodic Table
    To provide a single, representative average atomic-weight value for an element ignoring any material source uncertainties, the latest IUPAC recommendations include a concept of “conventional atomic weight value” whereby most or all atomic-weight variation in normal materials is covered (with an interval of ± 1 in the last digit).  PubChem has adopted this approach for the twelve elements (hydrogen, lithium, boron, carbon, nitrogen, oxygen, magnesium, silicon, sulfur, chlorine, bromine, and thallium) with standard atomic weights given as intervals.
  • Standard atomic weights updated
    Standard atomic weights in PubChem use the latest values provided by IUPAC (except when a conventional atomic weight value is used).  For the thirty-four elements without any abundance information (e.g., technetium), the atomic weight of the most stable, non-theoretical isotope was used, as found in the NuBase2012 evaluation (http://amdc.in2p3.fr/nubase/nubtab12.asc) of nuclear and decay properties.
  • Trimmed precision of molecular weights
    To take into account the uncertainties in elemental abundances and masses, the precision of all molecular weight values were reduced from six to three digits beyond the decimal point.
  • Updated allowed isotopes for elements
    The internal PubChem knowledgebase used to generate the PubChem Compound database from the PubChem Substance database was updated.  (Read this blog if you are not familiar with how these two databases differ from each other.)  As a part of this, only isotopes for elements with an experimentally measured half-life of one millisecond or greater were allowed when using the NuBase2012 evaluation of nuclear and decay properties (http://amdc.in2p3.fr/nubase/nubtab12.asc).  This (slightly) modifies the scope of what can be found in the PubChem Compound database.

 Where can you learn more about this topic?

To learn more about this topic, please read the following:

  • Atomic weights of the elements 2013 (IUPAC Technical Report)
    Meija et al., Pure Appl. Chem. 2016; 88(3): 265-291.
    doi: 10.1515/pac-2015-0305
  • Isotopic compositions of the elements 2013 (IUPAC Technical Report)
    Meija et al., Pure Appl. Chem. 2016; 88(3): 293-306.
    doi: 10.1515/pac-2015-0503

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