Force Field Calculations on the Structures of Transition Metal Complexes. 1. Application to Copper(II) Complexes in Square-Planar Coordination

Wiesemann, F.; Teipel, S.; Krebs, B.; Hoeweler, U.

doi:10.1021/ic00087a027

Cited by 33 publications

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“…Such effects cannot be described by radial interactions, but rather require the introduction of angular forces describing the energetics of the transition-metal d-shell. Most existing methods for including angular forces in simulations of metal ions have used assumed functional forms (Comba et al, 1995, Allured et al, 1991, Timofeeva et al, 1995, Wiesemann et al, 1994, Sayle et al, 1995, Sayle et al, 1997 based, for example on the observed structures of small complexes. A recently developed method (Landis et al, 1998) treats the environment-dependent energetics of transition metals via a valence-bond approach.…”

Section: Introductionmentioning

confidence: 99%

The Functional Form of Angular Forces around Transition Metal Ions in Biomolecules

Carlsson

Zapata

2001

Biophysical Journal

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A method for generating angular forces around sigma-bonded transition metal ions is generalized to treat pi-bonded configurations. The theoretical approach is based on an analysis of ligand-field and small-cluster Hamiltonians based on the moments of the electron state distribution. The functional forms that are obtained involve a modification of the usual expression of the binding energy as a sum of ligand-ligand interactions, which, however, requires very little increase in CPU time. The angular interactions have simple forms involving sin and cos functions, whose relative weights depend on whether the ligands are sigma- or pi-bonded. They describe the ligand-field stabilization energy to an accuracy of about 10%, and the interaction energy of covalently bonded systems to an accuracy of better than 4%. The resulting functional forms for the force field are used to model the structure of small clusters, including fragments of the copper blue protein structure. Large deviations from the typical square copper coordination are found when pi-bonded ligands are present.

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Section: Introductionmentioning

confidence: 99%

The Functional Form of Angular Forces around Transition Metal Ions in Biomolecules

Carlsson

Zapata

2001

Biophysical Journal

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“…AMBER force field lacks of all the parameters related to the copper atom. The necessary parameters were obtained from the literature (41, 42). To model the copper binding site we followed a bonded approach based on spectroscopic data of copper ligands obtained from ESR, optical and NMR measurements on the Cu(II)–peptide complexes.…”

Section: Resultsmentioning

confidence: 99%

Enzyme mimics complexing Cu(II) ion: structure–function relationships

Corazza

Scarpa

Vianello

et al. 1999

The Journal of Peptide Research

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Five peptides containing (His-X2)-His or (His-X3)-His motifs have been designed and synthesized to coordinate Cu(II). Structural information was obtained by various spectroscopic techniques and was used as constraint to search for local conformational energy minima by molecular mechanics. Thermodynamic stability constants of the Cu(II) chelates was obtained by 19F-NMR. The synthesized Cu(II)-peptide chelates were tested as catalysts of some important red-ox processes occuring in biological systems, in particular oxidation of ascorbate and dismutation of superoxide ion. The catalytic efficiency of the five chelates was much lower than that of ascorbate oxidase. On the contrary, two of them showed kinetic constants for superoxide dismutation about one order of magnitude lower than that of the enzyme Cu,Zn superoxide dismutase. In both cases, the catalytic properties were dependent on the peptide sequence. The relationships between structure and activity are discussed to find the structural parameters crucial for catalytic activity that can be modulated by appropriate design and synthesis of the peptides.

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“…Crystallographic data for various small inorganic copper complexes with different nitrogen-containing ligands [ 28 – 31 ] were used to establish upper and lower limits on these distance constraints. Copper-histidine nitrogen ligand distances in various copper amine oxidases, thought to have similar copper environments to that in LOX, are typically between 1.9 and 2.1 Å [ 19 – 22 ].…”

Section: Methodsmentioning

confidence: 99%

Modeling Cu(II) Binding to Peptides Using the Extensible Systematic Force Field

Ryvkin

Greenaway

2010

Bioinorganic Chemistry and Applications

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The utility of the extensible systematic force field (ESFF) was tested for copper(II) binding to a 34-amino-acid Cu(II) peptide, which includes five histidine residues and is the putative copper-binding site of lysyl oxidase. To improve computational efficiency, distance geometry calculations were used to constrain all combinations of three histidine ligands to be within bonding distance of the copper and the best results were utilized as starting structures for the ESFF computations. All likely copper geometries were modeled, but the results showed only a small dependence on the geometrical model in that all resulted in a distorted square pyramidal geometry about the copper, some of the imidazole rings were poorly oriented for ligation to the Cu(II), and the copper-nitrogen bond distances were too long. The results suggest that ESFF should be used with caution for Cu(II) complexes where the copper-ligand bonds have significant covalency and when the ligands are not geometrically constrained to be planar.

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Force Field Calculations on the Structures of Transition Metal Complexes. 1. Application to Copper(II) Complexes in Square-Planar Coordination

Cited by 33 publications

References 0 publications

The Functional Form of Angular Forces around Transition Metal Ions in Biomolecules

The Functional Form of Angular Forces around Transition Metal Ions in Biomolecules

Enzyme mimics complexing Cu(II) ion: structure–function relationships

Modeling Cu(II) Binding to Peptides Using the Extensible Systematic Force Field

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