Elemental Analysis Plugin

This manual gives you a walk-through on how to use the Elemental Analysis Plugin:

• Introduction

• Options

• References

Introduction

The Elemental Analysis Plugin calculates basic descriptors related to the elemental composition of a molecule.

The example below illustrates the analysis results for an input structure.

Fig. 1 Elemental Analysis result window example

Options

In the Elemental Analysis Options window you can set the following options:

• Type

  1. Molecular weight: average molecular weight calculated from the standard atomic weights.

  1. Exact molecular weight: monoisotopic mass calculated from the weights of the most abundant natural isotopes of the elements.

  1. Nominal mass: monoisotopic mass calculated from the rounded weights of the most abundant natural isotopes of the elements.

  2. Formula: chemical formula of the molecule according to the Hill system: 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 is taken into account and Polymer Formula is generated.

  3. Formula with charge: gives the chemical formula of the molecule including its formal charge and with separately listed isotopes according to the Hill system.

  4. Dot-disconnected formula: chemical formula of the molecule with the formulae of its fragment (e.g. salts, counter ions, solvent molecules) separated by dots

  5. Dot-disconnected formula with charge: chemical formula of the molecule including its formal charge with the formulae of its fragment (e.g. salts, counter ions, solvent molecules) separated by dots

  6. Mass spectrum: calculates the mass distribution of the input molecule(s) considering the relative abundance of the isotopes. The distribution is displayed as a spectrum, which is usually called the m/z:relative abundance spectrum in mass spectroscopy.

  7. Composition: elemental composition given in weight percentage (w/w %), calculated from the atomic masses.

  8. Atom count: number of all atoms in the molecule.

{info} For polymers mass, composition and atom count calculations are not available. NaN, N/A and -1 values are returned in these cases, respectively.

• Use D/T symbols for Deuterium/Tritium: if unchecked (default), isotopes of hydrogen are displayed as 2H and 3H; otherwise 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; otherwise the results are displayed in a scroll window.

Fig. 2 Elemental Analysis calculation options

{info} On atomic weights used in molecular mass calculations

From Marvin v. 14.7.28 we use the 2013 IUPAC atomic weights of the elements published here.

From Marvin v. 19.2 we use the 2017 IUPAC atomic weights of elements.

From Marvin v. 20.15 we use the 2019 IUPAC atomic weights of elements.

From Marvin v. 22.20 we use the 2021 IUPAC atomic weights of elements.

You can find older and up-to-date information about the used weights here and here.

{info} On using custom atomic weights for molecular mass calculations

The atomic weights used for molecular mass calculations can be customized by placing the custom weights in an elements.txt file. This custom file should be placed under the Chemaxon configuration folder of the user's system. In the absence of such a custom file, default weights are used by the plugin.

References

1. G. Audi, A.H.Wapstra, The 1995 update to the atomic mass evaluation, Nuclear Physics A, Vol. 595, Issue 4, pp. 409-480, 1995;

2. 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;