Metals & Charged Species

Metals and Charged Species

Charged Species

Examples of charged species are:  [Na+]  and  [Ca+2]  and  [O-]

The EPI Suite programs do not evaluate charged species with the charges....the charges (including the plus and minus signs and numbers) must be removed.  The current MS-Windows versions of the EPI Suite programs will automatically remove charges for some (but not all) of the metals that can be evaluated.

For example, if sodium acetate is entered as:

[Na+][O-]C(=O)C   ...   the programs will convert it to:  [Na]OC(=O)C

Metals

Metals are designated by the atomic symbol of the metal enclosed in square brackets.  The current versions of the EPI Suite programs can accept most metals.  However, the ability of the individual programs in EPI Suite to produce meaningful results for metals, and inorganics in general, varies. The intended application domain of EPI Suite is organic chemicals, and inorganic as well as organometallic chemicals generally can be considered outside the domain.

Examples of correct SMILES for metals:

[Al]                Aluminum

[As]                Arsenic

[Au]                Gold

[Be]                Beryllium

[Bi]                Bismuth

[Ca]                Calcium

[Fe]                Iron

[Hg]                Mercury

[K]                Potassium

[Li]                Lithium

[Mg]                Magnesium

[Na]                Sodium

[Ni]                Nickel

[Pt]                Platinum

[Sb]                Antimony

[Sn]                Tin

[Zn]                Zinc

[Zr]                Zirconium

In the EPI Suite programs, sodium, potassium and lithium can be entered without the square brackets.  Do not put charges in the brackets ... exclude charges unless the atom is entered in the form of a disconnected SMILES that can be evaluated.