Static and dynamic Jahn-Teller distortions in CuN6 complexes. Crystal structures and EPR spectra of complexes between copper(II) and rigid, tridentate cis,cis-1,3,5-triaminocyclohexane (tach: Cu(tach)2(ClO4)2, Cu(tach)2(NO3)2. Crystal structure of Ni(tach)2(NO3)2

Ammeter, J. H.; Buergi, H. B.; Gamp, E.; Meyer-Sandrin, V.; Jensen, William P.

doi:10.1021/ic50193a042

Cited by 137 publications

(81 citation statements)

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“…Evaluation yields RjT = 0.322 (24)A. This value may be compared with the corresponding .mean value for 13 CuN 6 complexes reported by Ammeter et al (1979), Rrr = 0-32 A. On the other hand, if Rrr is evaluated for statically distorted CuO6 octahedra from R 2= y r= lad 2 where Adi =di -do, and do = mean value of Cu--O distance, we find values ranging from 0.265-0.501 A for the examples cited in their Table 4 by Gallucci & Gerkin (1989).…”

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confidence: 60%

“…On the other hand, if Rrr is evaluated for statically distorted CuO6 octahedra from R 2= y r= lad 2 where Adi =di -do, and do = mean value of Cu--O distance, we find values ranging from 0.265-0.501 A for the examples cited in their Table 4 by Gallucci & Gerkin (1989). Thus, in contrast to the fuN6 cases discussed by Ammeter et al (1979), Rrr does not appear to be transferable from crystal to crystal for CuO6 octahedra in the cases cited.…”

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confidence: 67%

“…If, following Ammeter et al (1979), the square of the Jahn-Teller radius, Rrr, is written as R2T = Z6= 1 6 (Ad~rr = y6= l(Ad/2)obsd _ ~..i= l(Adi2)res and it is assumed that a reasonable estimate for the residual contribution 2 (Adi)res not related to the dynamic Jahn-Teller effect can be obtained by comparison with the corresponding ellipsoids in isostructural salts containing Ni n or Co n, we find (Ad~)r~= 2i-0Ni--o(2),co--o(2) = 43 (9) × 10-4/~2 [using the data from isomorphic hexaaquanickel(II) chlorate and bromate and hexaaquacobalt(II) bromate cited in the preceding paragraph]. Thus, in the present case, R~r = 6[AUcu--o(2) -43 (9) x 10 -4 A2].…”

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Structure of hexaaquacopper(II) bromate

Blackburn¹,

Gallucci²,

Gerkin³

1991

Acta Crystallogr C

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Abstract.[Cu(H20)6](BrO3)2, M,=427"44, cubic, Pa-3, a = 10.3240 (6) A, V = 1100.38 (4) A 3, Z = 4, Dx=2"580gcm -3, A(MoK~)=0.71073A, /~= 92.32 cm-l, F(000) = 828, T = 296 K, R = 0.038 for 336 unique reflections having I > trz. The single type of copper ion (site symmetry 3) is coordinated by six water-molecule O atoms, each at an observed distance of 2-079 (4)A, in an array which is virtually regular octahedral, the nominal 90 ° angles measuring 89.95 (15) and 90.05 (15) °. Thus, this is not a typical Cu" complex in which (consistent with a static JahnTeller effect) a distorted octahedral array displays '(2 + 2 + 2)' coordination; rather, it is the sixth strict example of a CuII static structure inconsistent with the Jahn-Teller theorem. The presence of a dynamic Jahn-Teller effect is supported by the data. The single type of bromate ion has an observed Br---O bond length 1.649 (3)A and O--Br--O bond angle 104.17 (15) °. The bromate ion was found to manifest rigid-body behavior but, consistent with a dynamic Jahn-Teller effect, the copper-oxygen complex did not. The Br---O bond length corrected for rigid-body motion is 1.663 A. Refinement of the positional parameters of the two inequivalent H atoms permitted a detailed analysis of hydrogen bonding, which occurs principally between the oxygen octahedra and the bromate groups. This structure is isomorphic with those of hexaaquanickel(II) chlorate, hexaaquacobalt(II) bromate and hexaaquanickel(II) bro-

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Structure of hexaaquacopper(II) bromate

Blackburn¹,

Gallucci²,

Gerkin³

1991

Acta Crystallogr C

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“…The finding for the X-ray values confirms the earlier conclusion that difference displacement parameters are generally more physically meaningful than the displacement parameters themselves. The phenomenon is due to the fact that the systematic errors in the ADPs vary little between atoms and cancel largely on taking differences (Ammeter et al, 1979;Chandrasekhar & Bü rgi, 1984).…”

Section: Bonds Involving An H Atom (D-h)mentioning

confidence: 99%

Hirshfeld Atom Refinement

Grabowsky

Woinska

Jayatilaka

2016

Journal of the Crystallographic Society of Japan

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Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using HartreeFock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints -even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogenatom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å 2 as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements -an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å .

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“…However, whenever the crystal structure suggests equal Cu-N bonds, the anisotropic displacement parameters (ADPs) have been shown to be unusual. Such ADPs have previously been studied with a semi-rigid body model by analyzing differences in meansquare displacement amplitudes along Cu-N bonds or with a model of dynamic, Jahn-Teller coupling (Ammeter et al, 1979;Falvello, 1997;Halcrow, 2003).…”

Section: Introductionmentioning

confidence: 99%

Temperature-dependent analysis of thermal motion, disorder and structures of tris(ethylenediamine)zinc(II) sulfate and tris(ethylenediamine)copper(II) sulfate

Smeets

Parois

Bürgi

et al. 2011

Acta Crystallogr Sect B

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The crystal structures of the title compounds have been determined in the temperature range 140-290 K for the zinc complex, and 190-270 K for the copper complex. The two structures are isostructural in the trigonal space group P " 3 31c with the sulfate anion severely disordered on a site with 32 (D 3 ) symmetry. This sulfate disorder leads to a disordered three-dimensional hydrogen-bond network, with the N-H atoms acting as donors and the sulfate O atoms as acceptors. The displacement parameters of the N and C atoms in both compounds contain disorder contributions in the out-of-ligand plane direction owing to ring puckering and/or disorder in hydrogen bonding. In the Zn compound the vibrational amplitudes in the bond directions are closely similar. Their differences show no significant deviations from rigid-bond behaviour. In the Cu compound, a (presumably) dynamic Jahn-Teller effect is identified from a temperature-independent contribution to the displacement ellipsoids of the N atom along the N-Cu bond. These conclusions derive from analyses of the atomic displacement parameters with the Hirshfeld test, with rigid-body models at different temperatures, and with a normal coordinate analysis. This analysis considers the atomic displacement parameters (ADPs) from all different temperatures simultaneously and provides a detailed description of both the thermal motion and the disorder in the cation. The Jahn-Teller radii of the Cu compound derived on the basis of the ADP analysis and from the bond distances in the statically distorted low-temperature phase [Lutz (2010). Acta Cryst. C66, m330-m335] are found to be the same.

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Static and dynamic Jahn-Teller distortions in CuN6 complexes. Crystal structures and EPR spectra of complexes between copper(II) and rigid, tridentate cis,cis-1,3,5-triaminocyclohexane (tach: Cu(tach)2(ClO4)2, Cu(tach)2(NO3)2. Crystal structure of Ni(tach)2(NO3)2

Cited by 137 publications

References 12 publications

Structure of hexaaquacopper(II) bromate

Structure of hexaaquacopper(II) bromate

Hirshfeld Atom Refinement

Temperature-dependent analysis of thermal motion, disorder and structures of tris(ethylenediamine)zinc(II) sulfate and tris(ethylenediamine)copper(II) sulfate

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