Systematic analysis of metal coordination sphere geometry from crystallographic data: a general method for detecting geometrical preferences, deformations and interconversion pathways

Howard, Judith A. K.; Copley, Royston C. B.; Yao, Jing Wen; Allen, Frank H.

doi:10.1039/a806820h

Cited by 10 publications

(7 citation statements)

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“…The atoms N2/O2/O3 and N1/ O1/O4 de®ne the two triangular faces of the prism and exhibit a dihedral angle of 4.81 (5) ; atom N3 caps the O1/O2/O3/O4 face, with NdÐN3 = 2.5144 (14) A Ê . The LÐMÐL geometric parameters in (I) are fairly typical for the CTP coordination environment (Howard et al, 1998;Yao et al, 2001). The other plausible option for a coordination polyhedron of (I) is a capped octahedron, although the distortions when attempting to ®t the atoms of (I) to this system are signi®cant.…”

Section: Commentmentioning

confidence: 99%

Triisothiocyanatotetrakis(triphenylphosphine oxide)neodymium(III)

et al. 2004

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Section: Commentmentioning

confidence: 99%

Triisothiocyanatotetrakis(triphenylphosphine oxide)neodymium(III)

et al. 2004

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“…CaL 6 are octahedral, but with much larger distortions, oct , than are found for any of the other metals Mg±Zn (see Table 1); this is easily understandable as a consequence of the greater size of the Ca ion. For CaL 7 , an analysis of the angular distortions, , from pentagonal bipyramid (PBP) and capped trigonal prism (CTP) has not been performed here, but Howard et al (1998) have described how this can be performed and have given distributions equivalent to PBP and CTP for all seven-coordinate Distributions of MÁ Á ÁO distances in the CSD (April 1999 release, R < 0.065) greater than the cutoff distances given in Table 2 (a). Effectively, for Mn II , Fe and Zn the distances shown here are longer than those usually regarded as bonding; for Cu II and Mn III distances in the range up to 2.6 A might well be regarded as normal bonding distances in ML 5 or ML 6 when Jahn±Teller distortion is taken into account.…”

Section: Calcium Complexesmentioning

confidence: 99%

“…The indicator of Zabrodsky et al (1993) is appropriate to any polyhedron and is the mean-square displacement of all the vertices from the nearest regular polyhedron. Howard et al (1998) have used a measure Rc(1) which measures angular distortions only, as a percentage of their mean values. The measure used here is very similar to Rc(1) ± it is the r.m.s.…”

Section: Introductionmentioning

confidence: 99%

The geometry of metal–ligand interactions relevant to proteins. II. Angles at the metal atom, additional weak metal–donor interactions

Harding

2000

Acta Crystallogr D Biol Crystallogr

107

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Geometrical data which could be of relevance in the structure determination, structure refinement, assessment or understanding of metalloproteins have been extracted from the Cambridge Structural Database (CSD). The CSD contains crystallographic data from 'small-molecule' structures determined by X-ray or neutron diffraction to an accuracy and precision much better than that of most current protein structure determinations. Structures of Mg, Mn, Fe, Cu and Zn complexes with ligands whose donor atoms may be only N, O, S or Cl have been selected and analysed in terms of the geometry of the metal coordination group - octahedral, tetrahedral, tetragonal pyramidal etc. The r.m.s. deviation of all the interbond angles around the metal atom provides a measure, delta, of the deviation from ideal geometry. Average values of delta are tabulated for the different metals in each type of complex. For simple non-chelated complexes of Mn, Fe and Zn, distortions of up to 5 degrees in octahedral complexes and 10 degrees in tetrahedral complexes are found to be normal and seem likely to be a consequence of packing effects, ligand bulk or intramolecular effects. Substantially larger distortions are found for some other metals and geometries and are common for chelated complexes. Brief comments on six-, seven- and eight-coordinate Ca complexes are included. Tables are also presented showing that for four- and five-coordinate complexes of Zn and Cu it is quite common to find additional weakly coordinated ligands, usually with N or O donor atoms and with M.N,O distances longer than a normal bond length but shorter than a van der Waals contact, e.g. in the range 2.4-3.0 A for Zn and 2.6-3.0 A for Cu. Although the contributions to bond valency or bonding energy of such interactions may not be great, their effect on geometry can be considerable; they can, for example, cause much larger distortions of tetrahedral Zn complexes than indicated above.

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“…Conversely, it provides more information on the nature of the distortion pathway than methods which provide a single parameter to quantify the overall distortion, e.g. continuous symmetry (Pinsky & Avnir, 1998), symmetry-constrained RMS (root-mean square) deviation (Dollase, 1974), polyhedral volume (Makovicky & Balic Zunic, 1998) or angle-based methods (Howard et al, 1998). As a result, the observed stereochemistries may be rationalized in terms of the d-electron Internal coordinates for (a) T d reference geometry and (b) con®gurations, inter-ligand repulsion and %-bonding effects discussed above.…”

Section: Introductionmentioning

confidence: 99%

Structure correlation study of four-coordinate copper(I) and (II) complexes

Raithby

Shields

Allen

et al. 2000

Acta Crystallogr Sect B

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The geometries of four-coordinate CuI and CuII complexes in the Cambridge Structural Database (CSD) have been analysed systematically and compared using symmetry-deformation coordinates and principal component analysis. The observed stereochemistries have been rationalized in terms of the d-electron configurations, interligand repulsion and pi-bonding effects. The results confirm that the majority of four-coordinate copper(I) complexes in the CSD adopt tetrahedral geometries and deviations from tetrahedral symmetry are caused by the presence of chelating ligands or by the incorporation of copper centres into dimeric or polymeric structures. Four-coordinate copper(II) complexes generally adopt geometries close to square planar; this is particularly evident for bis(chelate) complexes where pi-bonding is important. Distortions towards tetrahedral geometries are attributable to steric interactions of bulky substituents in the bidentate ligands.

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Systematic analysis of metal coordination sphere geometry from crystallographic data: a general method for detecting geometrical preferences, deformations and interconversion pathways

Cited by 10 publications

References 1 publication

Triisothiocyanatotetrakis(triphenylphosphine oxide)neodymium(III)

Triisothiocyanatotetrakis(triphenylphosphine oxide)neodymium(III)

The geometry of metal–ligand interactions relevant to proteins. II. Angles at the metal atom, additional weak metal–donor interactions

Structure correlation study of four-coordinate copper(I) and (II) complexes

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