Amr A. A. Attia

Spin state preference and bond formation/cleavage barriers in ferrous-dioxygen heme adducts: remarkable dependence on methodology

The electronic structure of oxy- and aqua-bound active sites of hemoglobin (Hb) and cytochrome P450 mono oxygenase (CYP450) are investigated by applying a wide range of DFT functionals including the pure BP86, the hybrid B3LYP and the recently developed hybrid meta-GGA (M06 family). Mixed descriptions of the electronic structure and widely differing order of spin-multiplet energies are obtained depending on the functional employed. A reproduction of the experimental singlet ground state of oxy Hb was achieved by all functionals: convergence to the unrestricted broken symmetry solution was favored, except for BP86 where a direct Kohn–Sham determinant wave function was found to have the lowest energy. Ferrous-dioxygen bond cleavage for both models clearly shows preference for charge separation with superoxide liberation in the case of CYP450 (thiolate axial ligand), in comparison to liberation of a clear oxygen molecule in case of Hb. Nitric oxide bound superoxide reductase (SOR) is also investigated, as a model with a known S = 3/2 spin state; results provided by B3LYP, M06 and M06L are shown to correlate well with experimental data whereas the performance of the MP2 method was relatively poor. Fe–N bond cleavage was shown to give insight into the mechanism of hydrogen peroxide liberation in SOR.

Fe–O versus O–O bond cleavage in reactive iron peroxide intermediates of superoxide reductase

It is generally accepted that the catalytic cycles of superoxide reductases (SORs) and cytochromes P450 involve a ferric hydroperoxo intermediate at a mononuclear iron center with a coordination sphere consisting of four equatorial nitrogen ligands and one axial cysteine thiolate trans to the hydroperoxide. However, although SORs and P450s have similar intermediates, SORs selectively cleave the Fe–O bond and liberate peroxide, whereas P450s cleave the O–O bond to yield a high-valent iron center. This difference has attracted the interest of researchers, and is further explored here. Meta hybrid DFT (M06-2X) results for the reactivity of the putative peroxo/hydroperoxo reaction intermediates in the catalytic cycle of SORs were found to indicate a high-spin preference in all cases. An exploration of the energy profiles for Fe–O and O–O bond cleavage in all spin states in both ferric and ferrous models revealed that Fe–O bond cleavage always occurs more easily than O–O bond cleavage. While O–O bond cleavage appears to be thermodynamically and kinetically unfeasible in ferric hydrogen peroxide complexes, it could occur as a minor (significantly disfavored) side reaction in the interaction of ferrous SOR with hydrogen peroxide.

Nonspherical Deltahedra in Low-Energy Dicarbalane Structures Testing the Wade–Mingos Rules: The Regular Icosahedron Is Not Favored for the 12-Vertex Dicarbalane

Theoretical studies on the dicarbalanes C2Al(n-2)Men (n = 7-14; Me = methyl) predict both carbon atoms to be located at degree 4 vertices of a central C2Al(n-2) deltahedron in the lowest energy structures. As a consequence, deltahedra having two degree 4 vertices, two degree 6 vertices, and eight degree 5 vertices rather than the regular icosahedron having exclusively degree 5 vertices are found for the 12-vertex dicarbalane C2Al10Me12. However, the lowest energy C2Al(n-2)Men (n = 7-11) structures are based on the same most spherical (closo) deltahedra as the corresponding deltahedral boranes. The lowest energy structures for the 13- and 14-vertex systems C2Al(n-2)Men (n = 13 and 14) are also deltahedra having exactly two degree 4 vertices for the carbon atoms. The six-vertex C2Al4Me6 system is exceptional since bicapped tetrahedral and capped square pyramidal structures with degree 3 vertices for the carbon atoms are energetically preferred over the octahedral structure suggested by the Wade-Mingos rules.

Computational Investigation of the Initial Two-Electron, Two-Proton Steps in the Reaction Mechanism of Hydroxylamine Oxidoreductase

Reported here is a computational study based on density functional theory that presents the first attempt to investigate the 2-electron 2-proton reaction of Fe(III)-H2NOH to Fe(III)-HNO in the catalytic cycle of hydroxylamine oxidoreductase-a multiheme-containing enzyme that catalyzes the conversion of hydroxylamine (HA) to nitrite in nitrifying bacteria. Two subsequent protonation events are proposed to initiate the process, of which the second is suggested to be concerted with a one-electron oxidation. The final one-electron oxidation is further proposed to be accompanied by a third deprotonation process, suggesting that Fe(III)-HNO may not be an isolable intermediate in the HAO catalytic cycle. Further explorations are suggested to be focused on the following steps in the catalytic cycle, the influence of the lateral substituents of the heme (and especially of the Cys and Tyr cross-links), the comparative study of hydrazine oxidation, the proton delivery network in the distal site and, possibly, on linkage isomerism.

Novel non-spherical deltahedra in trirhenaborane structures

The geometries and energetics of the trirhenaboranes Cp3Re3Bn−3Hn−3 (Cp = η5-C5H5; n = 5 to 12) have been investigated using density functional theory for comparison with the experimentally known oblatocloso dirhenaboranes Cp*2Re2Bn−2Hn−2 (Cp* = η5-Me5C5; n = 8 to 12). The low-energy Cp3Re3Bn−3Hn−3 (7 ≤ n ≤ 12) structures are found to be Re3Bn−3 deltahedra with internally bonded Re3 triangles. The rhenium atoms are generally located at degree 6 to 8 vertices representing sites of low local curvature and the boron atoms at degree 3 to 5 vertices representing sites of high local curvature. The Re–Re bonds in the Re3 triangles of such clusters typically range from 2.6 to 2.7 A if they are located on or near the deltahedral surface and from 2.8 to 3.0 A if they go through the interior of the deltahedron away from the surface. Such highly non-spherical structures, typically having little symmetry, are related to the oblatocloso structures of the dirhenaboranes. A low-energy, more nearly spherical 12-vertex Cp3Re3B9H9 structure, essentially degenerate with the global minimum, has an Re–Re–Re chain embedded in a deltahedron having degree 5 and 6 rhenium vertices and degree 4 and 5 boron vertices. Low-energy structures for the 5-vertex Cp3Re3B2H2 system are derived from a trigonal bipyramid. Similarly, low-energy 6-vertex Cp3Re3B3H3 structures have central Re3B3 bicapped tetrahedra.

Fe(III) – Sulfide interaction in globins: Characterization and quest for a putative Fe(IV)-sulfide species

The present study reports findings regarding the contrast between H2S interaction with bovine hemoglobin (Hb) and horse heart myoglobin (Mb), in terms of binding and dissociation kinetics, affinities, and mechanism. At pH9.5, oxidation of ferric-sulfide adducts in presence of no free sulfide, using hexachloroiridate as oxidant is examined using stopped-flow UV-vis, EPR, vibrational spectroscopy and mass spectrometry. Oxidation of the ferric-sulfide adduct in such conditions occurs with a putative unstable Fe(IV)-sulfide adduct as intermediate that finally leads to a paramagnetic ferric species with distinct EPR features. As detected by MS spectrometry, this final species appears to be a truncated form of globin at a distinct Tyr. In case of Hb, only β-chain is truncated at Tyr144.

Novel non-spherical deltahedra in tritungstaboranes related to the experimentally known Cp*3W3(H)B8H8

The geometries and energetics of tritungstaboranes Cp3W3(H)Bn−3Hn−3 (Cp = η5-C5H5; n = 5 to 12), related to the experimentally known Cp*3W3(H)B8H8 (Cp* = η5-Me5C5), have been investigated using density functional theory and coupled cluster calculations. Such low-energy structures have central W3Bn−3 deltahedra with superimposed bonded W3 triangles. The “extra” hydrogen atom either bridges a deltahedral edge or caps a deltahedral face containing at least one tungsten atom. The tungsten atoms are located at degree 5 to 7 vertices in regions of a relatively low surface curvature whereas the boron atoms are located at degree 3 to 5 vertices in regions of a relatively high surface curvature. The five lowest-energy structures of the 11-vertex tritungstaborane Cp3W3(H)B8H8 all have the same central W3B8 deltahedron and differ only by the location of the “extra” hydrogen atom. The isosceles W3 triangles in these structures have two long ∼3.0 A W–W edges through the inside of the deltahedron with the third shorter W–W edge of ∼2.7 to ∼2.8 A corresponding to a surface deltahedral edge. The five Cp3W3(H)B8H8 structures differ only by the location of the “extra” hydrogen atom. The lowest energy such structure has the “extra” hydrogen atom bridging the surface W–W bond and corresponds to the experimental Cp*3W3(H)B8H8 structure, as determined using X-ray crystallography.

Cyclopentadienylironphosphacarboranes: fragility of polyhedral edges in the 11-vertex system

The lowest energy CpFeCHP(CH3)Bn−3Hn−3 (n = 8 to 12) structures, including the experimentally known CpFeCHP(CH3)B8H8, have been investigated by density functional theory. The central FeCPBn−3 polyhedra in all of the lowest energy such structures are the most spherical closo deltahedra. The heteroatoms are so located to have adjacent iron and phosphorus atoms and non-adjacent phosphorus and carbon atoms. One of the Fe–B bonds from the degree 6 iron vertex in the 11-vertex CpFeCHP(CH3)B8H8 structure appears to be fragile, readily elongating to ∼3.1 A in one of the low-energy structures, consistent with experimental observation on this system.

Cyclopentadienylcobalt azaboranes violating the Wade–Mingos rules: a degree 3 vertex for the nitrogen atom

The experimentally realized chemistry of polyhedral azaboranes includes the very stable cobalt derivative CpCoNHB9H9, which has been synthesized and structurally characterized by X-ray crystallography. The structures and energetics of the complete series of cobaltaazaboranes CpCoNHBn−2Hn−2 have now been studied by density functional theory. Low-energy structures are found for the 8- and 9-vertex systems based on non-spherical deltahedra providing a degree 3 vertex for the nitrogen atom and thus violating expectations from the Wade–Mingos rules. Thus the lowest energy CpCoNHB6H6 structure is an antipodally bicapped octahedron with the nitrogen atom at a degree 3 vertex rather than the most spherical bisdisphenoid. For the 9-vertex CpCoNHB7H7 system the lowest energy structures are based on the most spherical tricapped trigonal prism. However, isomeric CpCoNHB7H7 structures at ∼13 kcal mol−1 in energy above these structures are found with a central capped bisdisphenoid having the nitrogen atom at the degree 3 capping vertex. In contrast to the 8- and 9-vertex systems, the low-energy CpCoNHBn−2Hn−2 structures for the 10 to 12 vertex systems are based on the most spherical deltahedra. For the 10- and 11-vertex systems all of the low-energy structures have the nitrogen atom at a degree 4 vertex. The predicted Co–N and Co–B distances in the lowest energy CpCoNHB9H9 structure are very close to the experimental values.

Metal–metal bonding in deltahedral dimetallaboranes and trimetallaboranes: a density functional theory study

Abstract The skeletal bonding topology as well as the Re=Re distances and Wiberg bond indices in the experimentally known oblatocloso dirhenaboranes Cp*2Re2Bn−2Hn−2 (Cp*=η5Me5C5, n=8–12) suggest formal Re=Re double bonds through the center of a flattened Re2Bn−2 deltahedron. Removal of a boron vertex from these oblatocloso structures leads to oblatonido structures such as Cp2W2B5H9 and Cp2W2B6H10. Similar removal of two boron vertices from the Cp2Re2Bn−2Hn−2 (n=8–12) structures generates oblatoarachno structures such as Cp2Re2B4H8 and Cp2Re2B7H11. Higher energy Cp2Re2Bn−2Hn−2 (Cp=η5-C5H5, n=8–12) structures exhibit closo deltahedral structures similar to the deltahedral borane dianions BnHn2−. The rhenium atoms in these structures are located at adjacent vertices with ultrashort Re≣Re distances similar to the formal quadruple bond found in Re2Cl82− by X-ray crystallography. Such surface Re≣Re quadruple bonds are found in the lowest energy PnRe2Bn−2Hn−2 structures (Pn=η5,η5-pentalene) in which the pentalene ligand forces the rhenium atoms to occupy adjacent deltahedral vertices. The low-energy structures of the tritungstaboranes Cp3W3(H)Bn−3Hn−3 (n=5–12), related to the experimentally known Cp*3W3(H)B8H8, have central W3Bn−3 deltahedra with imbedded bonded W3 triangles. Similar structures are found for the isoelectronic trirhenaboranes Cp3Re3Bn−3Hn−3. The metal atoms are located at degree 6 and 7 vertices in regions of relatively low surface curvature whereas the boron atoms are located at degree 3–5 vertices in regions of relatively high surface curvature. The five lowest-energy structures for the 11-vertex tritungstaborane Cp3W3(H)B8H8 all have the same central W3B8 deltahedron and differ only by the location of the “extra” hydrogen atom. The isosceles W3 triangles in these structures have two long ~3.0 Å W–W edges through the inside of the deltahedron with the third shorter W–W edge of ~2.7 to ~2.8 Å corresponding to a surface deltahedral edge.