The effect of the carbonyl moiety on the spin density delocalization in the iminoxy radicals. Hybrid density functional studies

Jaszewski, Adrian R.; Tabaka, Katarzyna; Jezierska, Julia; Kedzierska, Jadwiga

doi:10.1016/s0009-2614(02)01743-8

Cited by 6 publications

(1 citation statement)

References 25 publications

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“…However, this theory has been subject of debate. Quantum chemistry studies on gas phase cluster models (27)(28)(29)(30) have proposed that the binding-site geometry is stable for both oxidation states and that the strain imposed by the protein is low and comparable with that found in other metalloenzymes, e.g., alcohol dehydrogenase (24,28). These studies have also claimed that the increase in redox potential with respect to the solvated ion could be explained, at least qualitatively, in terms of ligand field properties only, and that the active-site contribution to the reorganization free energy (innersphere reorganization energy, inn ) accounts for almost the whole .…”

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Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa

Cascella

Magistrato

Tavernelli

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

140

164

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We have coupled hybrid quantum mechanics (density functional theory; Car-Parrinello)/molecular mechanics molecular dynamics simulations to a grand-canonical scheme, to calculate the in situ redox potential of the Cu 2؉ ؉ e ؊ 3 Cu ؉ half reaction in azurin from Pseudomonas aeruginosa. An accurate description at atomistic level of the environment surrounding the metal-binding site and finite-temperature fluctuations of the protein structure are both essential for a correct quantitative description of the electronic properties of this system. We report a redox potential shift with respect to copper in water of 0.2 eV (experimental 0.16 eV) and a reorganization free energy ‫؍‬ 0.76 eV (experimental 0.6 -0.8 eV). The electrostatic field of the protein plays a crucial role in fine tuning the redox potential and determining the structure of the solvent. The inner-sphere contribution to the reorganization energy is negligible. The overall small value is mainly due to solvent rearrangement at the protein surface.density functional theory ͉ electron transfer ͉ molecular dynamics ͉ reorganization energy E lectron transfer (ET) processes are ubiquitous chemical reactions that occur in a variety of essential biological functions, such as immune response, respiration, and photosynthesis (1-10). Among the different families of ET proteins, single-copper cupredoxins, also known as blue copper proteins, are particularly appealing for theoretical studies because of their relatively small size and the great availability of experimental measurements in the literature. Blue copper proteins exchange electrons among themselves or with other redox proteins, such as cytochrome c551 or nitrite reductase, using a protein-bound Cu metal ion, that can exist in the Cu(II) or Cu(I) redox states (11,12). The copper ion forms a type 1 Cu-binding site ( Fig. 1), which is characterized by a bright blue color, a narrow hyperfine splitting in the electron paramagnetic resonance (EPR) spectra, a high reduction potential (13-15), and a strong structural similarity between oxidized and reduced states (13-17). In fact, in both oxidation states, the copper ion is coordinated by a cysteine (Cys) thiolate group and two histidine (His) nitrogen atoms in a trigonal planar conformation. The coordination polyhedron is completed by one axial ligand, typically a methionine (Met) thioether group. In azurin, a backbone amide oxygen of a glycine (Gly) constitutes an additional axial ligand (18). The structural similarity between the two redox states provides an advantage for the functionality of these ET proteins, as the reorganization free energy () for the redox process is small [0.6-0.8 eV (17, 19)], allowing a high ET rate (20-23). This is not the case for solvated copper ions and synthetic Cu complexes, which tend to have large structural changes concurrent with any variation in their oxidation state (24). The origin of the low value of is still unclear. The initial hypothesis implied that the rigidity of the protein would force Cu(II) to be bound in a geomet...

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confidence: 99%

Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa

Cascella

Magistrato

Tavernelli

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

140

164

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Theoretical Characterisation of Phosphinyl Radicals and Their Magnetic Properties: g Matrix

Witwicki

2015

ChemPhysChem

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The g matrices (g tensors) of various phosphinyl radicals (R2 P(.) ) were calculated using the DFT and multireference configuration interaction (MRCI) methods. The g matrices were distinctly dependent on the molecular structure of the radical. To thoroughly examine this dependence, the contributions from individual atoms and excited states were calculated. The former revealed the gain from the phosphorus atom to be preeminent unless PO or PS bonds are present in the radical molecule. The contributions owing to excited states arising from electronic transitions between doubly occupied molecular orbitals and the SOMO were clearly positive, as in the case of semiquinone and niroxide radicals. The transitions from the phosphorus lone pair were of paramount importance. Surprisingly, unlike for semiquinones and nitroxides, a significant negative contribution was observed from excitations from the SOMO to unoccupied molecular orbitals. For radicals with PO bonds, this contribution to the g2 component was dominant.

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Fundamental Studies of Long- and Short-Range Electron Exchange Mechanisms between Electrodes and Proteins

Khoshtariya

2011

Modern Aspects of Electrochemistry

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The effect of the carbonyl moiety on the spin density delocalization in the iminoxy radicals. Hybrid density functional studies

Cited by 6 publications

References 25 publications

Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa

Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa

Theoretical Characterisation of Phosphinyl Radicals and Their Magnetic Properties: g Matrix

Fundamental Studies of Long- and Short-Range Electron Exchange Mechanisms between Electrodes and Proteins

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