Bond valence sum analysis of metal-ligand bond lengths in metalloenzymes and model complexes

Thorp, H. Holden

doi:10.1021/ic00035a012

Cited by 407 publications

(242 citation statements)

References 7 publications

Supporting

Mentioning

219

Contrasting

Order By: Relevance

“…In the molecule, the chelated five-membered ring (Cu1-N1-C8-C9-N2) and six-membered ring (Cu1-O1-C2-C1-C7-N1) also contribute to the stability of the complex. The bondvalence sum for the Cu center is calculated to be 2.2, which is close to the expected value of 2 [1]. A strong intramolecular OH···O hydrogen bond helps to stabilize the molecular conformation (O4H4B···O2 with 0.66(7) Å, 2.02(7) Å, 2.603(3) Å, 149(8)°).…”

Section: Discussionsupporting

confidence: 69%

Crystal structure of aqua-((E)-N-(2-(2-hydroxybenzylideneamino)ethyl)- 4-methylbenzenesulfonamide)-copper(II), Cu(H2O)(C16H17N2O3S)

Li¹,

Wei²,

Hu³

et al. 2007

Zeitschrift Für Kristallographie - New Crystal Structures

View full text Add to dashboard Cite

Source of materialThe sulfonamide Schiff base ligand (E)-N-(2-(2-hydroxybenzylideneamino)ethyl)-4-methylbenzenesulfonamide (L) was synthesized by reacting tosyl-ethylenediamine with one equivalent of salicylaldehyde in ethanol. It is formed as yellow crystals (m.p. 126-127°C). To 20 mL hot ethanol solution containing 0.214 g (1 mmol) L, 0.199 g Cu(CH3COO)2 · H2O (1 mmol) in 10 mL ethanol was added under stirring for 1 h. A dark green solution was formed and filtrated. The filtrate was left for slow evaporation. Dark green block-shaped crystals of the title compound were obtained after 2 weeks. Experimental detailsThe H atoms were located in difference maps. While the water H atom positions were refined, the other H atoms were fixed in idealized positions and refined as riding with Uiso(H) = 1.2U eq or 1.5Ueq. DiscussionIn the title crystal structure copper(II) atom is chelated by one unsymmetrical Schiff base ligand providing their amide, amine N atoms and phenolate O atom and one water molecule (figure, top). A distorted square planar CuN2O2 environment arises with the N1···N2 and O1···O4 distances (2.605 Å and 2.662 Å, respectively) shorter than the N1···O1 and N2···O4 distances (2.801 Å and 2.902 Å, respectively). The Cu1N1 distance (1.923 Å) is shorter than Cu1N2 (1.969 Å) suggesting that the imine nitrogen atom is a slightly better donor than amide nitrogen atom because the electron density is delocalized into the sulfonyl group. The Cu1O4(water) distance is longer than Cu1O1(phenolate). The four coordinated atoms (N2O2) are arranged in a cisconformation. In the molecule, the chelated five-membered ring (Cu1-N1-C8-C9-N2) and six-membered ring (Cu1-O1-C2-C1-C7-N1) also contribute to the stability of the complex. The bondvalence sum for the Cu center is calculated to be 2.2, which is close to the expected value of 2 [1]. A strong intramolecular OH···O hydrogen bond helps to stabilize the molecular conformation (O4H4B···O2 with 0.66(7) Å, 2.02(7) Å, 2.603(3) Å, 149(8)°). The resulting six-membered chelate ring (Cu1-N2-S1-O2···H4B-O4) is planar with a mean deviation of 0.0830 Å. The crystal packing may be further stabilized by CH···O, CH···p and p···p interactions (figure, middle). The resulting C12H12···O3 hydrogen bonds among different symmetric motifs link the structure in layers running parallel to the a axis and shows a centrosymmetric arrangement mode. In the structure, there are the two p···p interactions formed between two rings of one molecule and its symmetry equivalent by inversion (x,y,z). The Cg···Cg i distance is 3.515 Å, where Cg and Cg i are the centroids of ring 1 (Cu1-O1-C2-C1-C7-N1) and ring 2 (C10 Z. Kristallogr.

show abstract

Section: Discussionsupporting

confidence: 69%

Crystal structure of aqua-((E)-N-(2-(2-hydroxybenzylideneamino)ethyl)- 4-methylbenzenesulfonamide)-copper(II), Cu(H2O)(C16H17N2O3S)

Li¹,

Wei²,

Hu³

et al. 2007

Zeitschrift Für Kristallographie - New Crystal Structures

View full text Add to dashboard Cite

show abstract

“…The results for the native enzyme were similar, but most distances (1.61, 1.72, and 2.11 Å) were shorter, and the more remote atoms were not explicitly assigned to imidazoles but as N or O. In a later study [131], the distance information was used in a Bond Valence Sum Analysis (BVSA) [132], using known correlations between the valence, ligand distances, and ligand geometry of ions, to correct the coordination number initially found [42] from 6 to 5. If one considers one of the imidazole or N/O ligands from the initial interpretation to be redundant in the 5-coordinate geometry, this outcome is consistent with the crystallographic results, first for the VCPO from the fungus C.…”

Section: Vanadium Haloperoxidase Exafsmentioning

confidence: 91%

Vanadium haloperoxidases: From the discovery 30 years ago to X-ray crystallographic and V K-edge absorption spectroscopic studies

Leblanc

Vilter

Fournier

et al. 2015

Coordination Chemistry Reviews

124

View full text Add to dashboard Cite

In the environment, vanadium-dependent haloperoxidases (VHPO) are likely to play a key role in the production of biogenic organo-halogens. These enzymes contain vanadate as a prosthetic group, and catalyze, in the presence of hydrogen peroxide, the oxidation of halide ions (Cl -, Br -or I -). They are classified according to the most electronegative halide that they can oxidize. Since the first discovery of a vanadium bromoperoxidase in the brown alga Ascophyllum nodosum thirty years ago, structural and mechanistic studies have been mainly conducted on two types of VHPO, chloro-and bromoperoxidases, and more recently on a vanadium-dependent iodoperoxidase. In this review, we highlight the main progress obtained on the structure-function relation of these proteins, based on biochemistry, crystallography and X-ray absorption spectroscopy (XAS). The comparison of 3D protein structures of the different VHPO helped identify the residues that govern the molecular mechanisms of catalysis and specificity of VHPO. Vanadium K-edge XAS gave further important insight to understand the fine changes around the vanadium cofactor during the catalytic cycle. The combination of different structural approaches, at different scales of resolution, shed new light on biological vanadium coordination in the active site, and its importance for the catalytic cycle and halide specificity of vanadium haloperoxidases. Keywords (max 6)Vanadium-dependent haloperoxidase, vanadium coordination, crystallographic structure, structural evolution, oligomeric state, X-ray absorption spectroscopy on biological vanadium

show abstract

“…In addition, the bond valence sums calculation based on bond lengths determined by crystallography or EXAFS also predicted the Si state to contain two Mn(III) and two Mn(N) (Thorp, 1992). This method has successfully predicted the correct oxidation states of the metal ions in a variety of model compounds and metalloenzymes (Thorp, 1992).…”

Section: Ib32 the Results From Xasmentioning

confidence: 90%

Structural oxidation state studies of the manganese cluster in the oxygen evolving complex of photosystem II

Liang¹

1994

View full text Add to dashboard Cite

Bond valence sum analysis of metal-ligand bond lengths in metalloenzymes and model complexes

Cited by 407 publications

References 7 publications

Crystal structure of aqua-((E)-N-(2-(2-hydroxybenzylideneamino)ethyl)- 4-methylbenzenesulfonamide)-copper(II), Cu(H2O)(C16H17N2O3S)

Crystal structure of aqua-((E)-N-(2-(2-hydroxybenzylideneamino)ethyl)- 4-methylbenzenesulfonamide)-copper(II), Cu(H2O)(C16H17N2O3S)

Vanadium haloperoxidases: From the discovery 30 years ago to X-ray crystallographic and V K-edge absorption spectroscopic studies

Structural oxidation state studies of the manganese cluster in the oxygen evolving complex of photosystem II

Contact Info

Product

Resources

About