Adjusting Bond Spheres
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:
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Reference:
[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
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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:
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Reference:
[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
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