Elemental Analysis Plugin

Basic molecular values related to the elemental composition of the molecule are calculated by the Elemental Analysis plugin.

In the Elemental Analysis Options panel you can check different properties:

• Type
  • Mass: average molecular mass calculated from the standard atomic weights ¹.
  • Exact mass: monoisotopic mass calculated from the weights ² of the most abundant natural isotopes of the elements.
  • Formula: chemical formula of the molecule according to the Hill system ³: the number of carbon atoms is indicated first, the number of hydrogen atoms next, and then the number of all other chemical elements subsequently, in alphabetical order. Isotopes (like Deuterium and Tritium) are not listed separately but counted together (e.g., deuterium and tritium atoms are counted as hydrogens). When the formula contains no carbon, all the elements, including hydrogen, are listed alphabetically. If the molecule contains an SRU or Repeating Unit S-group, it will be taken into account and Polymer Formula will be generated.
    Note: For polymer structures, mass, composition, and atom count calculations are not available and will return NaN, N/A, and -1, respectively.
  • Isotope formula: chemical formula of the molecule listing isotopes separately according to the Hill system.
  • Dot-disconnected formula: chemical formula of the molecule(s) separating fragment formulas by dots (e.g. salts, counterions, solvent molecules etc. are present).
  • Dot-disconnected isotope formula: chemical formula of the molecule separating fragment formulas by dots and listing isotopes separately.
  • Composition: elemental composition given in weight percentage (w/w %) calculated from the atomic masses.
  • Isotope composition: elemental composition listing isotopes separately (w/w %).
  • Atom count: number of all atoms in the molecule.

The examples shown below illustrating the difference between formula types:

Multifragment Molecule with isotopes	SRU Polymer S-group	Polymer defined as Repeating units S-group

• Use D/T symbols for deuterium/Tritium: if unchecked (default), isotopes of hydrogen are displayed in formulas as 2H and 3H, if checked, D and T symbols are used.
• Single fragment mode: if unchecked (default), the calculation handles unlinked molecules together (e.g. salt molecules), summing up the masses of each component, if checked, the results are displayed in a scroll window.

The results are shown in a new window:

The contents of the text field can be copied to the clipboard by Ctrl+C, the structure field offers a context menu from MarvinView.

References

• Atom weights: M. E. Wieser, "Atomic weights of the elements 2005 (IUPAC Technical Report)" Pure Appl. Chem., Vol. 78, No. 11, pp. 2051-2066, 2006; doi
• Isotope weights: G.Audi and A.H.Wapstra, "The 1995 update to the atomic mass evaluation" Nuclear Physics A595 vol. 4, pp. 409-480, 1995; doi
• The Hill system: E. A. Hill, "On A System Of Indexing Chemical Literature; Adopted By The Classification Division Of The U. S. Patent Office". J. Am. Chem. Soc., 22(8), pp. 478-494, 1900; doi