Application of DFT Methods in the Study of V^IVO²⁺–Peptide Interactions

Abstract

VIVO2+ complexes formed by histidylglycylglycine (HisGlyGlyH), glycylglycylhistidine (GlyGlyHisH), glycylglycylcysteine (GlyGlyCysH2), N‐glycyl‐bis(imidazol‐2‐yl)methylamine (Gly–BIMA), N‐glycyl‐bis(pyridin‐2‐yl)methylamine (Gly–BPMA), salicylglycyl‐L‐alanine (SalGly‐L‐AlaH2) and 1,2‐bis(2‐hydroxybenzamido)benzene (H2hybeb) in their fully deprotonated form were studied by density functional theory (DFT) methods. They are characterised by different total electric charges, total equatorial charges and number of V–N–amide bonds. DFT calculations enable structural features, like V–donor bond lengths, and spectroscopic features, like electron paramagnetic resonance (EPR) and electronic absorption parameters, to be calculated. The results suggest that an amide group coordinates vanadium in the“amide‐” rather than the “imine‐like” form with the nitrogen atom negatively charged and with a double bond between the carbon and oxygen atoms of the carbonyl group, and that the equatorial charge is delocalised among all the donors bound to vanadium (Ooxido included). The analysis of the molecular orbital composition reveals that the dxy orbital is the vanadium orbital at lower energy, that it can participate in a π bond with the nitrogen pz orbital of the amide groups, that the vanadium dxz and dyz orbitals are involved in a large π interaction with the oxido px and py orbitals and that differences in the donor strengths of the ligands and deviations from the ideal square‐pyramidal symmetry can result in the separation of the energies of the vanadium dxz and dyz orbitals.

Oxidovanadium(IV) complexes involving dehydroacetic acid and β-diketones of bioinorganic and medicinal relevance: Their synthesis, characterization, thermal behavior and DFT aspects

“…From the overall composition the weakest bond is with H 2 O reflected from bond length data as well as from orbital composition. The results are in good agreement as per the reports appeared elsewhere [70][71][72].…”

The effect of the functional, basis set, and solvent in the simulation of the geometry and spectroscopic properties of VIVO2+ complexes. chemical and biological applications

“…Several approaches were used: for example, Saladino and Larsen used a scalar relativistic, spin‐unrestricted, open‐shell Kohm‐Sham calculation for simulating A N for seven V IV O 2+ species,67 whereas Neese showed that for Cu 2+ complexes hybrid functionals, such as B3LYP or PWP1, give better predictions than functionals based on the generalized gradient approximation like BP or BLYP 66b. In the absence of systematic DFT studies regarding V IV O 2+ species, we recently performed preliminary simulations at different level of theory, and the best results have been obtained with half‐and‐half hybrid functional BHandH, whereas the choice of the basis set, 6‐311+g(d,p) or 6‐311g(d,p), is less important 68. The results are illustrated in Figure 8.…”

Vanadium and proteins: Uptake, transport, structure, activity and function

“…This approach was used to characterize the active site, the catalytic cycle and the structure of other metal proteins [157] and consists in the simulation of the 51 V hyperfine coupling tensor A of a V IV O complex which can be considered a model for the active site. When 51 V A is calculated using the functional BHandHLYP and the basis set 6-311g(d,p), a good model of the V sites should give A z values in agreement with the experimental one with a deviation around 2-3% [158,159,160,161,162,163,164]. Therefore, DFT methods may be used to predict A z for a V IV O 2+ species, and vice versa, to predict an unknown structure from its A z value.…”