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<title>GAMGI Interfaces: Atom Modify</title>
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<h1>Atom Modify</h1>
<div id="notebook">
<ul>
<li><a href="modify_element.html">Element</a></li>
<li><span>Property</span></li>
<li><a href="modify_analysis.html">Analysis</a></li>
<li><a href="modify_position.html">Position</a></li>
<li><a href="modify_view.html">View</a></li>
<li><a href="modify_length.html">Length</a></li>
<li><a href="modify_angle.html">Angle</a></li>
</ul>
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<div class="contents">
Change here the properties of an atom (or list of atoms,
previously selected with Atom->Select, when <b>Global</b> is pressed).
Parameters for empty entries or <b>Local</b> choices remain unchanged.
<h3>Mass</h3>
The <b>Mass</b> 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 or undefined (for dummy atoms, Du, this
is the default). All elements have a known mass.
<p/>
To define new default values, select <b>Atom->Config</b> (check
<b>Help->Interfaces->Atom->Config</b>) or import XML configuration
files (check <b>Help->Formats->Atom->Config</b>).
<p/>
Pressing <b>List</b>, a new dialog shows a list with the more important
isotope mass information, taken from <a href="http://www.wikipedia.com/">
http://www.wikipedia.com/</a>, 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).
<h3>Radius</h3>
The <b>Radius</b> entry sets the atomic radius. The default values are the
effective covalent radius. Radius must always be positive or undefined (for
dummy atoms, <b>Du</b>, this is the default). 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
<b>Bond->Create</b>.
<p/>
To define new default values, select <b>Atom->Config</b> (check
<b>Help->Interfaces->Atom->Config</b>) or import XML configuration files
(check <b>Help->Formats->Atom->Config</b>).
<p/>
Pressing <b>List</b>, a new dialog shows a list with the more important
radius data, taken from <a href="http://www.webelements.com/">
http://www.webelements.com/</a> (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:
<p/>
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.
<p/>
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.
<p/>
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.
<p/>
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.
<p/>
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.
<p/>
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.
<p/>
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.
<p/>
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.
<h3>Charge</h3>
The <b>Charge</b> entry sets the atomic charge. The default is <b>0.0.</b>
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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