GAMGI Interfaces: Atom Create

# Atom Create

- Element
- Property
- Analysis
- Position
- View

Set here the atom properties.

### Mass

The Mass entry sets the atomic mass. The default value is the so called atomic weight, the average of all naturally occurring isotopes, weighted by their natural abundances, or, when these do not exist, the isotope with a longer half-life time (not necessarily the easiest to synthetize and more common). Mass must always be positive (for dummy atoms, Du, the default is the H value). All elements have a known mass.

To define new default values, select Atom->Config (check Help->Interfaces->Atom->Config) or import XML configuration files (check Help->Formats->Atom->Config).

Pressing List, a new dialog shows a list with the more important isotope mass information, taken from http://www.wikipedia.com/, after comparison with other sources. This list contains all naturally occurring isotopes, with their relative abundances, plus all the isotopes with a half-life longer than one year (all elements until Cf except At, Rn, Fr), or, when these do not exist, one day (Rn, plus Es, Fm, Md), one hour (At, Lr, Rf, Db), one minute (Fr, No, Sg) or one second (Bh, Hs, Mt, Ds, Rg). Some isotopes have both a natural abundance and a half life decay, necessarily very long. Some isotopes correspond to excited states (Rh, Ag, Sn, Ta, Re, Ir, Bi, Am).

Abundances are given in percentages, half-lifes are given in years y, days d, hours h, minutes m and seconds s. Isotopes that exist in the excited state are signaled with an asterisk.

### Radius

The Radius entry sets the atomic radius. The default values are the effective covalent radius. Radius must always be positive (for dummy atoms, Du, the default is the H value). Some elements do not have a known radius: Pm, At, Rn, Fr, Es, Fm, Md, No, Lr, Rf, Db, Sg, Bh, Hs, Mt, Ds, Rg. In this case, the default comes from the nearest element, with a smaller atomic number, with a known radius. Atomic radius are also used to define default minimum and maximum distance limits for bond creation, as discussed in Bond->Create.

To define new default values, select Atom->Config (check Help->Interfaces->Atom->Config) or import XML configuration files (check Help->Formats->Atom->Config).

Pressing List, a new dialog shows a list with the more important radius data, taken from http://www.webelements.com/ (where the original publications are referenced), except the ionic radius, taken directly from Shannon's paper, Acta Cryst. A32, 751 (1976). The radius listed are:

1) Half distance between atoms in its element natural state, (most from L.E. Sutton (Ed.), Table of interatomic distances and configuration in molecules and ions, Supplement 1956-1959, Special publication No. 18, Chemical Society, London, UK, 1965.). Available up to Cf (98), except Pm, At, Rn, Fr.

2) Effective atomic (from J.C. Slater, J. Chem. Phys. 1964, 39, 3199), empirically derived by comparison of bond lengths in over 1200 bond types in ionic, metallic, and covalent crystals and molecules. Available up to Am (95) except He, Ne, Kr, Xe, At, Rn, Fr.

3) Calculated atomic (from E. Clementi, D.L.Raimondi, and W.P. Reinhardt, J. Chem. Phys. 1963, 38, 2686), obtained from SCF ab-initio calculations. Available up to Rn (86) except La, Ce.

4) Effective covalent (including from R.T. Sanderson in Chemical Periodicity, Reinhold, New York, USA, 1962.), empirically obtained by comparing distances between single-bonded equal atoms. Available for all elements up to La (57), plus Lu (71) to Bi (83) plus Rn.

5) Calculated covalent, (from Beatriz Cordero et al, in "Covalent radii revisited", Dalton Trans., 2008), arguably more consistent than the effective covalent radius. Available up to Cm (96). For C, there are radius available for sp3, sp2 and sp hybridization. For Mn, Fe, Co there are radius available for low (LS) and high (HS) spin configurations.

6) Van der Waals (mainly from A. Bondi, J. Phys. Chem., 1964, 68, 441.), established from contact distances between non-bonding atoms in touching molecules or atoms.

7) Ionic effective (from R.D. Shannon, Acta Cryst. A32, 751, 1976.), empirically derived from about 1000 distances, taken mainly from oxide and fluoride structures, plus a range of correlations. These radius are a function of valence, coordination, mass (for H) and low (LS) and high (HS) electronic spin (for Cr, Mn, Fe, Co, Ni). Available for all elements up to Cf (98) expect He, Ne, Ar, Kr, Rn.

To get the so-called ionic crystalline radius, suggested by Fumi and Tosi and published also by Shannon, just sum 0.14 to the cation and subtract 0.14 to the anion, so the cation-anion distance remain unchanged. According to Shannon, it is felt that these crystal radii correspond more closely to the physical size of ions in a solid. However, they might less efective in predicting the cation coordination by using Pauling's first rule.

### Charge

The Charge entry sets the atomic charge. The default is 0.0. but all real values are valid. The most common way to use charges is to attribute previously calculated values to different atoms, construct atomic structures with these atoms, and then export these structures to files, to feed Molecular Mechanics programs requiring charge potentials.
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