Diamond 2.1: Adjusting bond spheres
Diamond 2.1 Features Overview...
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Diamond can create bonds without bonding informations in the input
file. The bonding spheres are calculated from mean bond length resources or
from effective radii.
Especially for metal-organic structures, the bonding spheres between metal and
C, O, N, etc., may be too short or too long. For that reason, Diamond
offers a very versatile histogram to adjust these spheres (the "connectivity"):
After checking the connectivity for example in Bis(triphenylphosphineiminium)
15-carbonylpentaosmium carbide iodide [1], the molecule creation function
generates a picture like this in one single step:
The selection of bonding spheres as well as the adjustment of the sphere sizes
can also be applied to inorganic structures that contain molecular subunits,
like in the mineral beryl [2]. After the import of the structural parameters,
Si-O, Be-O, and Al-O automatically have been pre-defined as connected.
Disabling bonds between Al and O as well as between Be and O leads to discrete
Si6O18 rings, whereas these units can be connected by
enabling the bonds between Al and O. Be and O are not connected in this
example:
References:
[1] Name: Bis(triphenylphosphineiminium) 15-carbonylpentaosmium carbide iodide
Formula: (((C6H5)3 P)2 N) (Os5
C(CO)15 I)
Author(s): Jackson P F, Johnson B F G, Lewis J, Nicholls J N, McPartlin M,
Nelson W J H
Title: Synthesis of the Carbido Anion (Os5 C (CO)15 I)
and the X-Ray Crystal Structures of Os5 C (CO)15 and ((Ph3
P)2 N) (Os5 C (CO)15 I)
Journal: JCCCA 1980 (1980), pp. 564 - 566
[2] ICSD Collection Code 2791
Name: Aluminium beryllium hexasilicate hydrate *
Formula: Al2 Be3 (SiO3)6 (H2O)0.0991
Author(s): Morosin, B
Title: Structure and thermal expansion of beryl
Journal: ACBCAR 28 (1972), pp. 1899 - 1903
Mineral name: Beryl
Diamond 2.1 Features Overview...
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