Shuqiang Niu

Georgetown University, Washington, Washington, D.C., United States

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Publications (36)145.05 Total impact

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    ABSTRACT: Broken-symmetry density functional theory (BS-DFT) calculations are assessed for redox energetics [Cu(SCH3)2](1-/0), [Cu(NCS)2](1-/0), [FeCl4](1-/0), and [Fe(SCH3)4](1-/0) against vertical detachment energies (VDE) from valence photoelectron spectroscopy (PES), as a prelude to studies of metalloprotein analogs. The M06 and B3LYP hybrid functionals give VDE that agree with the PES VDE for the Fe complexes, but both underestimate it by ∼400 meV for the Cu complexes; other hybrid functionals give VDEs that are an increasing function of the amount of Hartree-Fock (HF) exchange and so cannot show good agreement for both Cu and Fe complexes. Range-separated (RS) functionals appear to give a better distribution of HF exchange since the negative HOMO energy is approximately equal to the VDEs but also give VDEs dependent on the amount of HF exchange, sometimes leading to ground states with incorrect electron configurations; the LRC-ωPBEh functional reduced to 10% HF exchange at short-range give somewhat better values for both, although still ∼150 meV too low for the Cu complexes and ∼50 meV too high for the Fe complexes. Overall, the results indicate that while HF exchange compensates for self-interaction error in DFT calculations of both Cu and Fe complexes, too much may lead to more sensitivity to nondynamical correlation in the spin-polarized Fe complexes.
    Journal of Chemical Theory and Computation 03/2014; 10(3):1283-1291. · 5.39 Impact Factor
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    ABSTRACT: The oxidation-reduction potentials of electron transfer proteins determine the driving forces for their electron transfer reactions. Although the type of redox site determines the intrinsic energy required to add or remove an electron, the electrostatic interaction energy between the redox site and its surrounding environment can greatly shift the redox potentials. Here, a method for calculating the reduction potential versus the standard hydrogen electrode, E°, of a metalloprotein using a combination of density functional theory and continuum electrostatics is presented. This work focuses on the methodology for the continuum electrostatics calculations, including various factors that may affect the accuracy. The calculations are demonstrated using crystal structures of six homologous HiPIPs, which give E° that are in excellent agreement with experimental results. © 2012 Wiley Periodicals, Inc.
    Journal of Computational Chemistry 11/2012; · 3.84 Impact Factor
  • Yan Luo, Shuqiang Niu, Toshiko Ichiye
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    ABSTRACT: Determining the redox energetics of redox site analogues of metalloproteins is essential in unraveling the various contributions to electron transfer properties of these proteins. Since studies of the [4Fe-4S] analogues show that the energies are dependent on the ligand dihedral angles, broken symmetry density functional theory (BS-DFT) with the B3LYP functional and double-ζ basis sets calculations of optimized geometries and electron detachment energies of [1Fe] rubredoxin analogues are compared to crystal structures and gas-phase photoelectron spectroscopy data, respectively, for [Fe(SCH(3))(4)](0/1-/2-), [Fe(S(2)-o-xyl)(2)](0/1-/2-), and Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) in different conformations. In particular, the study of Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) is the only direct comparison of calculated and experimental gas phase detachment energies for the 1-/2- couple found in the rubredoxins. These results show that variations in the inner sphere energetics by up to ∼0.4 eV can be caused by differences in the ligand dihedral angles in either or both redox states. Moreover, these results indicate that the protein stabilizes the conformation that favors reduction. In addition, the free energies and reorganization energies of oxidation and reduction as well as electrostatic potential charges are calculated, which can be used as estimates in continuum electrostatic calculations of electron transfer properties of [1Fe] proteins.
    The Journal of Physical Chemistry A 08/2012; 116(35):8918-24. · 2.77 Impact Factor
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    ABSTRACT: Many quantum mechanical calculations indicate water molecules in the gas and liquid phase have much larger quadrupole moments than any of the common site models of water for computer simulations. Here, comparisons of multipoles from quantum mechanical∕molecular mechanical (QM∕MM) calculations at the MP2∕aug-cc-pVQZ level on a B3LYP∕aug-cc-pVQZ level geometry of a waterlike cluster and from various site models show that the increased square planar quadrupole can be attributed to the p-orbital character perpendicular to the molecular plane of the highest occupied molecular orbital as well as a slight shift of negative charge toward the hydrogens. The common site models do not account for the p-orbital type electron density and fitting partial charges of TIP4P- or TIP5P-type models to the QM∕MM dipole and quadrupole give unreasonable higher moments. Furthermore, six partial charge sites are necessary to account reasonably for the large quadrupole, and polarizable site models will not remedy the problem unless they account for the p-orbital in the gas phase since the QM calculations show it is present there too. On the other hand, multipole models by definition can use the correct multipoles and the electrostatic potential from the QM∕MM multipoles is much closer than that from the site models to the potential from the QM∕MM electron density. Finally, Monte Carlo simulations show that increasing the quadrupole in the soft-sticky dipole-quadrupole-octupole multipole model gives radial distribution functions that are in good agreement with experiment.
    The Journal of Chemical Physics 04/2011; 134(13):134501. · 3.12 Impact Factor
  • Shuqiang Niu, Toshiko Ichiye
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    ABSTRACT: A central issue in understanding redox properties of iron–sulphur (Fe–S) proteins is determining the factors that tune the reduction potentials of the Fe–S clusters. Studies of redox site analogues play an important role, particularly because individual factors can be examined independently of the environment by combining calculations and experiments of carefully designed ligands for the analogues. For iron–sulphur analogues, our study has shown that broken-symmetry density functional theory gives good energetics when the geometry is optimised using B3LYP with a double-ζ basis set with polarisation functions, and the energies of these geometries are calculated using B3LYP with additional diffuse functions added to the sulphurs. A comparison of our calculated energies for redox site analogues in the gas phase against electron detachment energies measured by a combination of electrospray ionisation and photoelectron spectroscopy (EI–PES) by Wang and co-workers has been essential because the comparison is for exactly the same molecule with no approximation for the environment. Overall, the correlation of our B3LYP/ 6-31(++)SG**//B3LYP/6-31G** detachment energies with EI–PES experiments is excellent for a wide variety of analogues. Moreover, our calculations at this level have provided insight into a wide variety of properties of iron–sulphur proteins.
    Molecular Simulation 01/2011; 37(7):572-590. · 1.06 Impact Factor
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    ABSTRACT: ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
    ChemInform 08/2010; 30(33).
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    ABSTRACT: α,β-Unsaturated thioaldehydes and thioketones, R1CHCH−C(S)R2, are prepared in situ by the reaction between the corresponding carbonyl compounds and bis(dimethylaluminum) sulfide. These compounds undergo [4 + 2] self-dimerization reactions in which one molecule serves as the heterodiene component and the other as the dienophile to afford different types of dimeric products depending on the R1 and R2: 1,2-dithiin and 1,3-dithiin (R1 = R2 = H), 1,2-dithiin (R1 = Ph, R2 = H, CH3), or dihydrothiopyran (R1 = R2 = Ph). These differences in selectivity are explained on the basis of the relative energies evaluated by molecular orbital (MO) calculations at the DFT (density functional theory) level. The calculations show that in the dimerization reaction of thioacrolein (I), the head-to-tail (S−C−S bonded) dimers are kinetically more stable by about 5 kcal/mol but slightly thermodynamically unstable by about 2 kcal/mol than the head-to-head (S−S bonded) dimers. The calculations on thiocinnamaldehyde (IV) indicate that the dimerization reactions of phenyl-substituted α,β-unsaturated thioaldehydes and thioketones are almost equally controlled by thermodynamic and kinetic factors. These unsaturated thiocarbonyl compounds also function as heterodienes (CC−CS) in the cycloaddition reaction with norbornadiene and as dienophiles (CS) in the reaction with cyclopentadiene.
    ChemInform 01/2010; 32(7).
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    ABSTRACT: Quantum chemical calculations of metal clusters in proteins for redox studies require both computational feasibility as well as accuracies of at least ∼50 mV for redox energies but only ∼0.05 Å for bond lengths. Thus, optimization of spin-unrestricted density functional theory (DFT) methods, especially the hybrid generalized gradient approximation functionals, for energies while maintaining good geometries is essential. Here, different DFT functionals with effective core potential (ECP) and full core basis sets for [Fe(SCH(3))(4)](2-/1-) and [Fe(SCH(3))(3)](1-/0), which are analogs of the iron-sulfur protein rubredoxin, are investigated in comparison to experiment as well as other more computationally intensive electron correlation methods. In particular, redox energies are calibrated against gas-phase photoelectron spectroscopy data so no approximations for the environment are needed. B3LYP gives the best balance of accuracy in energy and geometry compared B97gga1 and BHandH and is better for energies than Møller-Plesset perturbation theory series (MP2, MP3, MP4SDQ) and comparable to coupled cluster [CCSD, CCSD(T)] methods. Of the full core basis sets tested, the 6-31G** basis sets give good geometries, and addition of diffuse functions to only the sulfur significantly improves the energies. Moreover, a basis set with an ECP on only the iron gives a less accurate but still reasonable geometries and energies.
    Journal of Chemical Theory and Computation 05/2009; 5(5):1361-1368. · 5.39 Impact Factor
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    Shuqiang Niu, Toshiko Ichiye
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    ABSTRACT: The large differences in redox potentials between the HiPIPs and ferredoxins are generally attributed to hydrogen bonds and electrostatic effects from the protein and solvent. Recent ligand K-edge X-ray absorption studies by Solomon and co-workers show that the Fe-S covalencies of [4Fe-4S] clusters in the two proteins differ considerably apparently because of hydrogen bonds from water, indicating electronic effects may be important. However, combined density function theory (DFT) and photoelectron spectroscopy studies by our group and Wang and co-workers indicate that hydrogen bonds tune the potential of [4Fe-4S] clusters by mainly electrostatics. The DFT studies here rationalize both results, namely that the observed change in the Fe-S covalency is due to differences in ligand conformation between the two proteins rather than hydrogen bonds. Moreover, the ligand conformation affects the calculated potentials by approximately 100 mV and, thus, is a heretofore unconsidered means of tuning the potential.
    Journal of the American Chemical Society 05/2009; 131(16):5724-5. · 10.68 Impact Factor
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    Shuqiang Niu, Toshiko Ichiye
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    ABSTRACT: The cleavage of [4Fe-4S]-type clusters is thought to be important in proteins such as Fe-S scaffold proteins and nitrogenase. However, most [4Fe-4S](2+) clusters in proteins have two antiferromagnetically coupled high-spin layers in which a minority spin is delocalized in each layer, thus forming a symmetric Fe(2.5+)-Fe(2.5+) pair, and how cleavage occurs between the irons is puzzling because of the shared electron. Previously, we proposed a novel mechanism for the fission of a [4Fe-4S] core into two [2Fe-2S] cores in which the minority spin localizes on one iron, thus breaking the symmetry and creating a transition state with two Fe(3+)-Fe(2+) pairs. Cleavage first through the weak Fe(2+)-S bonds lowers the activation energy. Here, we propose a test of this mechanism: break the symmetry of the cluster by changing the ligands to promote spin localization, which should enhance reactivity. The cleavage reactions for the homoligand [Fe(4)S(4)L(4)](2-) (L = SCH(3), Cl, H) and heteroligand [Fe(4)S(4)(SCH(3))(2)L(2)](2-) (L = Cl, H) clusters in the gas phase were examined via broken-symmetry density functional theory calculations. In the heteroligand clusters, the minority spin localized on the iron coordinated by the weaker electron-donor ligand, and the reaction energy and activation barrier of the cleavage were lowered, which is in accord with our proposed mechanism and consistent with photoelectron spectroscopy and collision-induced dissociation experiments. These studies suggest that proteins requiring facile fission of their [4Fe-4S] cluster in their biological function might have spin-localized [4Fe-4S] clusters.
    The Journal of Physical Chemistry A 05/2009; 113(19):5710-7. · 2.77 Impact Factor
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    Shuqiang Niu, Toshiko Ichiye
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    ABSTRACT: A central issue in understanding redox properties of iron-sulfur proteins is determining the factors that tune the reduction potentials of the Fe-S clusters. Recently, Solomon and coworkers have shown that the Fe-S bond covalency of protein analogs measured by %L, the percent ligand character of the Fe 3d orbitals, from ligand K-edge X-ray absorption spectroscopy (XAS) correlates with the electrochemical redox potentials. Also, Wang and coworkers have measured electron detachment energies for iron-sulfur clusters without environmental perturbations by gas-phase photoelectron spectroscopy (PES). Here the correlations of the ligand character with redox energy and %L character are examined in [Fe(4)S(4)L(4)](2-) clusters with different ligands by broken symmetry density functional theory (BS-DFT) calculations using the B3LYP functional together with PES and XAS experimental results. These gas-phase studies assess ligand effects independently of environmental perturbations and thus provide essential information for computational studies of iron-sulfur proteins. The B3LYP oxidation energies agree well with PES data, and the %L character obtained from natural bond orbital analysis correlates with XAS values, although it systematically underestimates them because of basis set effects. The results show that stronger electron-donating terminal ligands increase %L(t), the percent ligand character from terminal ligands, but decrease %S(b), the percent ligand character from the bridging sulfurs. Because the oxidized orbital has significant Fe-L(t) antibonding character, the oxidation energy correlates well with %L(t). However, because the reduced orbital has varying contributions of both Fe-L(t) and Fe-S(b) antibonding character, the reduction energy does not correlate with either %L(t) or %S(b). Overall, BS-DFT calculations together with XAS and PES experiments can unravel the complex underlying factors in the redox energy and chemical bonding of the [4Fe-4S] clusters in iron-sulfur proteins.
    The Journal of Physical Chemistry A 05/2009; 113(19):5671-6. · 2.77 Impact Factor
  • Shuqiang Niu, Toshiko Ichiye
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    ABSTRACT: In biological electron transport chains, [2Fe–2S] clusters have versatile electrochemical properties and serve as important electron carriers in a wide variety of biological processes. To understand structural effects on the variation in reduction potentials in [2Fe–2S] proteins, a series of [2Fe–2S] protein analogs with bidentate ligands (−SC 2 H 4 NH 2) were recently produced by collision-induced dissociation of [Fe 4 S 4(L)4]2− (L = SC 2 H 4 NH 2). Combined with photoelectron spectroscopy findings, the reaction mechanisms of [Fe 4 S 4(L)4]2− to [Fe 2 S 2(L)2]− and the structural effects of ligands on the electronic and redox properties of the [2Fe–2S] clusters are investigated here using broken-symmetry density functional theory method. Our calculations suggest that [Fe 2 S 2(η2−L)(cis−L)]− and [Fe 2 S 2(η2−L)2]− are the experimentally observed [2Fe–2S] products, which are generated via a fission process of [Fe 4 S 4(L)4]2− followed by rearrangement of ligands of [Fe 2 S 2(L)2]−. Moreover, structural variation of the ferrous center may dramatically affect the oxidation energy of the [2Fe–2S] clusters.
    Theoretical Chemistry Accounts 01/2007; 117(2):275-281. · 2.14 Impact Factor
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    ABSTRACT: A unique π-conjugative interaction pattern was experimentally revealed in the doubly acetylide-bridged binuclear group 4 metallocene complexes, which was involved in C–C coupling/cleavage reactions of acetylides and σ-alkynyl migrations. To elucidate how this multi-center bonding network affects the structural and reaction properties of these complexes, density functional theory (DFT) calculations and molecular orbital (MO) analysis were carried out on the electronic structure and σ-alkynyl migration mechanisms of the doubly acetylide-bridged binuclear Zr complexes, (L2Zr)2(μ-CCH)2 (L=Cp,Cl). The B3LYP calculations suggested that the doubly [σ,π] acetylide-bridged complex C2h-(L2Zr)2(μ-CCH)2 was produced by the reaction of L2Zr(CCH)2 with L2Zr through a C2v-(L2Zr)2(μ-CCH)2 intermediate followed by an isomerization process. In particular, the isomerization of C2h- or C2v-(L2Zr)2(μ-CCH)2 is almost thermoneutral through a low barrier of 15.3–17.0kcal/mol. The MO Walsh diagram revealed that the two isomers have a very similar six-center-six-electron bonding network. The coplanar π-conjunctive interaction by the electron donating and back-donating interactions between the metal centers and acetylide ligands significantly stabilizes the doubly acetylide-bridged binuclear group 4 metallocene complexes and the isomerization transition state.
    Journal of Organometallic Chemistry - J ORGANOMET CHEM. 01/2007; 692(21):4760-4767.
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    ABSTRACT: Using potentially bidentate ligands (-SC2H4NH2), we produced [2Fe-2S]+ species of different coordination geometries by fission of [4Fe-4S]2+ complexes. Even though the ligands are monodentate in the cubane complexes, both mono- and bidentate complexes were observed in the [2Fe] fission products through self-assembly because of the high reactivity of the tricoordinate iron sites. The electronic structure of the [2Fe] species was probed using photoelectron spectroscopy and density functional calculations. It was found that tetracoordination significantly decreases the electron binding energies of the [2Fe] complexes, thus increasing the reducing capability of the [2Fe-2S]+ clusters.
    Inorganic Chemistry 04/2005; 44(5):1202-4. · 4.59 Impact Factor
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    ABSTRACT: To probe how H-bonding effects the redox potential changes in Fe-S proteins, we produced and studied a series of gaseous cubane-type analogue complexes, [Fe(4)S(4)(SEt)(3)(SC(n)H(2n+1))](2-) and [Fe(4)S(4)(SEt)(3)(SC(n)H(2n)OH)](2-) (n = 4, 6, 11; Et = C(2)H(5)). Intrinsic redox potentials for the [Fe(4)S(4)](2+/3+) redox couple involved in these complexes were measured by photoelectron spectroscopy. The oxidation energies from [Fe(4)S(4)(SEt)(3)(SC(n)H(2n)OH)](2-) to [Fe(4)S(4)(SEt)(3)(SC(n)H(2n)OH)](-) were determined directly from the photoelectron spectra to be approximately 130 meV higher than those for the corresponding [Fe(4)S(4)(SEt)(3)(SC(n)H(2n+1))](2-) systems, because of the OH...S hydrogen bond in the former. Preliminary Monte Carlo and density functional calculations showed that the H-bonding takes place between the -OH group and the S on the terminal ligand in [Fe(4)S(4)(SEt)(3)(SC(6)H(12)OH)](2-). The current data provide a direct experimental measure of a net H-bonding effect on the redox potential of [Fe(4)S(4)] clusters without the perturbation of other environmental effects.
    Journal of the American Chemical Society 01/2005; 126(48):15790-4. · 10.68 Impact Factor
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    ABSTRACT: Assembly and disassembly of protein-bound iron-sulfur clusters are involved in a wide variety of vital biological processes, ranging from stabilization of protein structures to signaling and sensing of environmental conditions such as changes of Fe or O2 concentrations.
    Journal of Physical Chemistry A - J PHYS CHEM A. 01/2004; 108(32):6750-6757.
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    ABSTRACT: The cubane [4Fe-4S] is the most common multinuclear metal center in nature for electron transfer and storage. Using electrospray, we produced a series of gaseous doubly charged cubane-type complexes, [Fe4S4L4]2- (L = -SC2H5, -SH, -Cl, -Br, -I) and the Se-analogues [Fe4Se4L4]2- (L = -SC2H5, -Cl), and probed their electronic structures with photoelectron spectroscopy and density functional calculations. The photoelectron spectral features are similar among all the seven species investigated, revealing a weak threshold feature due to the minority spins on the Fe centers and confirming the low-spin two-layer model for the [4Fe-4S](2+) core and its "inverted level scheme". The measured adiabatic detachment energies, which are sensitive to the terminal ligand substitution, provide the intrinsic oxidation potentials of the [Fe4S4L4]2- complexes. The calculations revealed a simple correlation between the electron donor property of the terminal thiolate as well as the bridging sulfide with the variation of the intrinsic redox potentials. Our data provide intrinsic electronic structure information of the [4Fe-4S] cluster and the molecular basis for understanding the protein and solvent effects on the redox properties of the [4Fe-4S] active sites.
    Journal of the American Chemical Society 12/2003; 125(46):14072-81. · 10.68 Impact Factor
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    ABSTRACT: We report a photoelectron spectroscopy (PES) and theoretical study on a series of transition metal halide complexes: FeX4− and MX3− (M = Mn, Fe, Co, Ni, X = Cl, Br). PES spectra were obtained at two photon energies (193 and 157 nm), revealing the complicated electronic structures of these metal complexes and their variation with the ligand-field geometry and metal center substitution. Density functional calculations were carried out to obtain information about the structures, energetics, and molecular orbitals of the metal complexes and used to interpret the PES spectra. For the tetrahedrally coordinated ferric complexes (FeX4−), the PES data directly confirm the “inverted level scheme” electronic structure, where the Fe 3d electrons lie below those of the ligands due to a strong spin-polarization of the Fe 3d levels. For the three-coordinate complexes (MX3−), the calculations also revealed strong spin polarizations, but the molecular orbital diagrams present a “mixed level scheme,” in which the ligand orbitals and the Fe 3d majority spin orbitals are spaced closely in the same energy regions. This “mixed level scheme” is due to the larger splitting of the 3d orbitals in the stronger D3h ligand field and the smaller spin polarizations of the divalent metal centers. The calculations show that the metal 3d orbitals are stabilized gradually relative to the ligand orbitals from Mn to Ni in the tri-halide complexes consistent with the PES spectral patterns. © 2003 American Institute of Physics.
    The Journal of Chemical Physics 10/2003; 119(16):8311-8320. · 3.12 Impact Factor
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    ABSTRACT: Iron−sulfur proteins are an important class of electron carriers in a wide variety of biological reactions. Determining the intrinsic contribution of the metal site to the redox potential is crucial in understanding how the protein environment influences the overall redox properties of the Fe−S proteins. Here we combine density functional theory and coupled cluster methods with photodetachment spectroscopy to study the electronic structures and gas-phase redox potentials of the [Fe(SCH3)4]2-/-/0 and [Fe(SCH3)3]-/0 analogues of the rubredoxin redox site. The calculations show that oxidations of [Fe(SCH3)4]2- and [Fe(SCH3)4]- involve mainly the Fe 3d and S 3p orbitals, respectively. The calculated adiabatic and vertical detachment energies are in good agreement with the experiment for [Fe(SCH3)3]- and [Fe(SCH3)4]-. The current results further confirm the “inverted level scheme” for the high-spin [1Fe] systems. The redox couple, [Fe(SCH3)4]-/2-, which is the one found in rubredoxin, but cannot be accessed experimentally in the gas phase, was investigated using a thermodynamic cycle that relates it to the [Fe(SCH3)3]-/0 couple and the ligand association reaction, [Fe(SCH3)3]0/- + SCH3- → [Fe(SCH3)4]-/2-. The calculated reduction energy of [Fe(SCH3)4]- (1.7 eV) compares well with the value (1.6 eV) estimated from the calculated bond energies and the experimental detachment energy of [Fe(SCH3)3]-. Thus, this thermodynamic cycle method can be used to estimate metal−ligand bonding energies and determine intrinsic reduction potentials from photodetachment experiments when the reduced forms are not stable in the gas phase.
    The Journal of Physical Chemistry A 04/2003; 107(16):2898-2907. · 2.77 Impact Factor
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    ABSTRACT: We report the observation of symmetric fission in doubly charged Fe-S cluster anions, [Fe(4)S(4)X(4)](2-)-->2[Fe(2)S(2)X(2)](-) (X=Cl,Br), owing to both Coulomb repulsion and antiferromagnetic coupling. Photoelectron spectroscopy shows that both the parent and the fission fragments have similar electronic structures and confirms the inverted energy schemes due to the strong spin polarization of the Fe 3d levels. The current observation provides direct confirmation for the unusual spin couplings in the [Fe(4)S(4)X(4)](2-) clusters, which contain two valent-delocalized and ferromagnetically coupled Fe2S2 subunits.
    Physical Review Letters 10/2002; 89(16):163401. · 7.73 Impact Factor

Publication Stats

266 Citations
145.05 Total Impact Points

Institutions

  • 2007–2014
    • Georgetown University
      • Department of Chemistry
      Washington, Washington, D.C., United States
  • 2000–2010
    • Texas A&M University
      • Department of Chemistry
      College Station, Texas, United States
  • 2002–2005
    • Washington State University
      • School of Molecular Biosciences
      Pullman, WA, United States
  • 1999
    • Kanazawa University
      Kanazawa, Ishikawa, Japan