Formation of a Pd@Au₁₂ Superatomic Core in Au₂₄Pd₁(SC₁₂H₂₅)₁₈ Probed by ¹⁹⁷Au Mössbauer and Pd K‑Edge EXAFS Spectroscopy

Recently, a variety of thiolated gold alloy clusters with well-defined compositions have been synthesized, and the effect of doping on their properties and stability has been studied extensively. We examined the occupation site of the Pd dopant within Au₂₄Pd₁(SC₁₂H₂₅)₁₈ by probing complementarily the local environments of Au and Pd elements using ¹⁹⁷Au Mössbauer and Pd K-edge EXAFS spectroscopy, respectively. The experimental results suggest that the doped single Pd atom is preferentially located at the center of Au₂₄Pd₁(SC₁₂H₂₅)₁₈ to form the superatomic Pd@Au₁₂ core, which supports recent theoretical predictions. These spectroscopic measurements also clarified intracluster electron transfer from the Pd atom to the surrounding Au atoms

Axial Ligand Effects on Vibrational Dynamics of Iron in Heme Carbonyl Studied by Nuclear Resonance Vibrational Spectroscopy

Nuclear resonance vibrational spectroscopy (NRVS) and density functional theory calculation (DFT) have been applied to illuminate the effect of axial ligation on the vibrational dynamics of iron in heme carbonyl. The analyses of the NRVS data of five- (5c) and six-coordinate (6c) heme–CO complexes indicate that the prominent feature of ⁵⁷Fe partial vibrational density of state (⁵⁷FePVDOS) at the 250–300 cm^–1 region is significantly affected by the association of the axial ligand. The DFT calculations predict that the prominent ⁵⁷FePVDOS is composed of iron in-plane motions which are coupled with porphyrin pyrrole in-plane (ν₄₉, ν₅₀, and ν₅₃), an out-of-plane (γ₈) (two of four pyrrole rings include the in-plane modes, while the rest of pyrrole rings vibrate along the out-of-plane coordinate), and out-of-phase carbonyl C and O atom displacement perpendicular to the Fe–C–O axis. Thus, in the case of the 5c CO–heme the prominent ⁵⁷FePVDOS shows sharp and intense feature because of the degeneracy of the <i>e</i> symmetry mode within the framework of <i>C</i>_4<i>v</i> symmetry molecule, whereas the association of the axial imidazole ligand in the 6c complex with the lowered symmetry results in split of the degenerate vibrational energy as indicated by broader and lower intensity features of the corresponding NRVS peak compared to the 5c structure. The vibrational energy of the iron in-plane motion in the 6c complex is higher than that in 5c, implying that the iron in the 6c complex includes stronger in-plane interaction with the porphyrin compared to 5c. The iron in-plane mode above 500 cm^–1, which is predominantly coupled with the out-of-phase carbonyl C and O atom motion perpendicular to Fe–C–O, called as Fe–C–O bending mode (δ_Fe–C–O), also suggests that the 6c structure involves a larger force constant for the <i>e</i> symmetry mode than 5c. The DFT calculations along with the NRVS data suggest that the stiffened iron in-plane motion in the 6c complex can be ascribed to diminished pseudo-Jahn–Teller instability along the <i>e</i> symmetry displacement due to an increased <i>a</i>₁–<i>e</i> orbital energy gap caused by σ* interaction between the iron d_<i>z</i>² orbital and the nitrogen p orbital from the axial imidazole ligand. Thus, the present study implicates a fundamental molecular mechanism of axial ligation of heme in association with a diatomic gas molecule, which is a key primary step toward versatile biological functions

Nuclear Resonance Vibrational Spectroscopic Definition of Peroxy Intermediates in Nonheme Iron Sites

Fe^III-(hydro)­peroxy intermediates have been isolated in two classes of mononuclear nonheme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well-defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement. Here, we present the NRVS spectra of side-on Fe^III-peroxy and end-on Fe^III-hydroperoxy model complexes and assign these spectra using calibrated DFT calculations. We then use DFT calculations to define and understand the changes in the NRVS spectra that arise from protonation and from opening the Fe–O–O angle. This study identifies four spectroscopic handles that will enable definition of the binding mode and protonation state of Fe^III-peroxy intermediates in mononuclear nonheme Fe enzymes. These structural differences are important in determining the frontier molecular orbitals available for reactivity

NRVS Studies of the Peroxide Shunt Intermediate in a Rieske Dioxygenase and Its Relation to the Native Fe^II O₂ Reaction

The Rieske dioxygenases are a major subclass of mononuclear nonheme iron enzymes that play an important role in bioremediation. Recently, a high-spin Fe^III–(hydro)­peroxy intermediate (BZDOp) has been trapped in the peroxide shunt reaction of benzoate 1,2-dioxygenase. Defining the structure of this intermediate is essential to understanding the reactivity of these enzymes. Nuclear resonance vibrational spectroscopy (NRVS) is a recently developed synchrotron technique that is ideal for obtaining vibrational, and thus structural, information on Fe sites, as it gives complete information on all vibrational normal modes containing Fe displacement. In this study, we present NRVS data on BZDOp and assign its structure using these data coupled to experimentally calibrated density functional theory calculations. From this NRVS structure, we define the mechanism for the peroxide shunt reaction. The relevance of the peroxide shunt to the native Fe^II/O₂ reaction is evaluated. For the native Fe^II/O₂ reaction, an Fe^III–superoxo intermediate is found to react directly with substrate. This process, while uphill thermodynamically, is found to be driven by the highly favorable thermodynamics of proton-coupled electron transfer with an electron provided by the Rieske [2Fe-2S] center at a later step in the reaction. These results offer important insight into the relative reactivities of Fe^III–superoxo and Fe^III–hydroperoxo species in nonheme Fe biochemistry