29 research outputs found
The X-ray Absorption Spectroscopic Model of the Copper(II) Imidazole Complex Ion in Liquid Aqueous Solution: A Strongly Solvated Square Pyramid
Cu K-edge extended X-ray absorption fine structure (EXAFS)
and
Minuit X-ray absorption near-edge structure (MXAN) analyses were combined
to evaluate the structure of the copperĀ(II) imidazole complex ion
in liquid aqueous solution. Both methods converged to the same square-pyramidal
inner coordination sphere [CuĀ(Im)<sub>4</sub>L<sub>ax</sub>]<sup>2+</sup> (L<sub>ax</sub> indeterminate) with four equatorial nitrogen atoms
at EXAFS, 2.02 Ā± 0.01 Ć
, and MXAN, 1.99 Ā± 0.03 Ć
.
A short-axial N/O scatterer (L<sub>ax</sub>) was found at 2.12 Ā±
0.02 Ć
(EXAFS) or 2.14 Ā± 0.06 Ć
(MXAN). A second but
very weak axial CuāN/O interaction was found at 2.9 Ā±
0.1 Ć
(EXAFS) or 3.0 Ā± 0.1 Ć
(MXAN). In the MXAN fits,
only a square-pyramidal structural model successfully reproduced the
doubled maximum of the rising K-edge X-ray absorption spectrum, specifically
excluding an octahedral model. Both EXAFS and MXAN also found eight
outlying oxygen scatterers at 4.2 Ā± 0.3 Ć
that contributed
significant intensity over the entire spectral energy range. Two prominent
rising K-edge shoulders at 8987.1 and 8990.5 eV were found to reflect
multiple scattering from the 3.0 Ć
axial scatterer and the imidazole
rings, respectively. In the MXAN fits, the imidazole rings took in-plane
rotationally staggered positions about copper. The combined (EXAFS
and MXAN) model for the unconstrained cupric imidazole complex ion
in liquid aqueous solution is an axially elongated square-pyramidal
core, with a weak nonbonded interaction at the second axial coordination
position and a solvation shell of eight nearest-neighbor water molecules.
This core square-pyramidal motif has persisted through [CuĀ(H<sub>2</sub>O)<sub>5</sub>]<sup>2+</sup>, [CuĀ(NH<sub>3</sub>)<sub>4</sub>(NH<sub>3</sub>,H<sub>2</sub>O)]<sup>2+</sup>,, and now [CuĀ(Im)<sub>4</sub>L<sub>ax</sub>)]<sup>2+</sup> and appears to be the geometry
preferred by unconstrained aqueous-phase copperĀ(II) complex ions
Substrate and Metal Control of Barrier Heights for Oxo Transfer to Mo and W Bis-dithiolene Sites
Reaction coordinates for oxo transfer from the substrates
Me<sub>3</sub>NO, Me<sub>2</sub>SO, and Me<sub>3</sub>PO to the biologically
relevant MoĀ(IV) bis-dithiolene complex [MoĀ(OMe)Ā(mdt)<sub>2</sub>]<sup>ā</sup> where mdt = 1,2-dimethyl-ethene-1,2-dithiolateĀ(2-),
and from Me<sub>2</sub>SO to the analogous WĀ(IV) complex, have been
calculated using density functional theory. In each case, the reaction
first proceeds through a transition state (TS1) to an intermediate
with substrate weakly bound, followed by a second transition state
(TS2) around which breaking of the substrate XāO bond begins.
By analyzing the energetic contributions to each barrier, it is shown
that the nature of the substrate and metal determines which transition
state controls the rate-determining step of the reaction
Substrate and Metal Control of Barrier Heights for Oxo Transfer to Mo and W Bis-dithiolene Sites
Reaction coordinates for oxo transfer from the substrates
Me<sub>3</sub>NO, Me<sub>2</sub>SO, and Me<sub>3</sub>PO to the biologically
relevant MoĀ(IV) bis-dithiolene complex [MoĀ(OMe)Ā(mdt)<sub>2</sub>]<sup>ā</sup> where mdt = 1,2-dimethyl-ethene-1,2-dithiolateĀ(2-),
and from Me<sub>2</sub>SO to the analogous WĀ(IV) complex, have been
calculated using density functional theory. In each case, the reaction
first proceeds through a transition state (TS1) to an intermediate
with substrate weakly bound, followed by a second transition state
(TS2) around which breaking of the substrate XāO bond begins.
By analyzing the energetic contributions to each barrier, it is shown
that the nature of the substrate and metal determines which transition
state controls the rate-determining step of the reaction
Spin-Polarization-Induced Preedge Transitions in the Sulfur KāEdge XAS Spectra of Open-Shell Transition-Metal Sulfates: Spectroscopic Validation of ĻāBond Electron Transfer
Sulfur K-edge X-ray
absorption spectroscopy (XAS) spectra of the monodentate sulfate complexes
[M<sup>II</sup>(itao)Ā(SO<sub>4</sub>)Ā(H<sub>2</sub>O)<sub>0,1</sub>] (M = Co, Ni, Cu) and [CuĀ(Me<sub>6</sub>tren)Ā(SO<sub>4</sub>)] exhibit
well-defined preedge transitions at 2479.4, 2479.9, 2478.4, and 2477.7
eV, respectively, despite having no direct metalāsulfur bond,
while the XAS preedge of [ZnĀ(itao)Ā(SO<sub>4</sub>)] is featureless.
The sulfur K-edge XAS of [CuĀ(itao)Ā(SO<sub>4</sub>)] but not of [CuĀ(Me<sub>6</sub>tren)Ā(SO<sub>4</sub>)] uniquely exhibits a weak transition
at 2472.1 eV, an extraordinary 8.7 eV below the first inflection of
the rising K-edge. Preedge transitions also appear in the sulfur K-edge
XAS of crystalline [M<sup>II</sup>(SO<sub>4</sub>)Ā(H<sub>2</sub>O)]
(M = Fe, Co, Ni, and Cu, but not Zn) and in sulfates of higher-valent
early transition metals. Ground-state density functional theory (DFT)
and time-dependent DFT (TDDFT) calculations show that charge transfer
from coordinated sulfate to paramagnetic late transition metals produces
spin polarization that differentially mixes the spin-up (Ī±)
and spin-down (Ī²) spin orbitals of the sulfate ligand, inducing
negative spin density at the sulfate sulfur. Ground-state DFT calculations
show that sulfur 3p character then mixes into metal 4s and 4p valence
orbitals and various combinations of ligand antibonding orbitals,
producing measurable sulfur XAS transitions. TDDFT calculations confirm
the presence of XAS preedge features 0.5ā2 eV below the rising
sulfur K-edge energy. The 2472.1 eV feature arises when orbitals at
lower energy than the frontier occupied orbitals with S 3p character
mix with the copperĀ(II) electron hole. Transmission of spin polarization
and thus of radical character through several bonds between the sulfur
and electron hole provides a new mechanism for the counterintuitive
appearance of preedge transitions in the XAS spectra of transition-metal
oxoanion ligands in the absence of any direct metalāabsorber
bond. The 2472.1 eV transition is evidence for further radicalization
from copperĀ(II), which extends across a hydrogen-bond bridge between
sulfate and the itao ligand and involves orbitals at energies below
the frontier set. This electronic structure feature provides a direct
spectroscopic confirmation of the through-bond electron-transfer mechanism
of redox-active metalloproteins
LāEdge Xāray Absorption Spectroscopic Investigation of {FeNO}<sup>6</sup>: Delocalization vs Antiferromagnetic Coupling
NO is a classic non-innocent ligand,
and iron nitrosyls can have
different electronic structure descriptions depending on their spin
state and coordination environment. These highly covalent ligands
are found in metalloproteins and are also used as models for FeāO<sub>2</sub> systems. This study utilizes iron L-edge X-ray absorption
spectroscopy (XAS), interpreted using a valence bond configuration
interaction multiplet model, to directly experimentally probe the
electronic structure of the <i>S</i> = 0 {FeNO}<sup>6</sup> compound [FeĀ(PaPy<sub>3</sub>)ĀNO]<sup>2+</sup> (PaPy<sub>3</sub> = <i>N,N</i>-bisĀ(2-pyridylmethyl)Āamine-<i>N</i>-ethyl-2-pyridine-2-carboxamide) and the <i>S</i> = 0 [FeĀ(PaPy<sub>3</sub>)ĀCO]<sup>+</sup> reference compound. This method allows separation
of the Ļ-donation and Ļ-acceptor interactions of the ligand
through ligand-to-metal and metal-to-ligand charge-transfer mixing
pathways. The analysis shows that the {FeNO}<sup>6</sup> electronic
structure is best described as Fe<sup>III</sup>āNOĀ(neutral),
with no localized electron in an NO Ļ* orbital or electron hole
in an Fe dĻ orbital. This delocalization comes from the large
energy gap between the FeāNO Ļ-bonding and antibonding
molecular orbitals relative to the exchange interactions between electrons
in these orbitals. This study demonstrates the utility of L-edge XAS
in experimentally defining highly delocalized electronic structures
A Zinc Linchpin Motif in the MUTYH Glycosylase Interdomain Connector Is Required for Efficient Repair of DNA Damage
Mammalian MutY glycosylases have
a unique architecture that features
an interdomain connector (IDC) that joins the catalytic N-terminal
domain and 8-oxoguanine (OG) recognition C-terminal domain. The IDC
has been shown to be a hub for interactions with protein partners
involved in coordinating downstream repair events and signaling apoptosis.
Herein, a previously unidentified zinc ion and its coordination by
three Cys residues of the IDC region of eukaryotic MutY organisms
were characterized by mutagenesis, ICP-MS, and EXAFS. <i>In vitro</i> kinetics and cellular assays on WT and Cys to Ser mutants have revealed
an important function for zinc coordination on overall protein stability,
ironāsulfur cluster insertion, and ability to mediate DNA damage
repair. We propose that this āzinc linchpinā motif serves
to structurally organize the IDC and coordinate the damage recognition
and base excision functions of the C- and N-terminal domains
Iron LāEdge Xāray Absorption Spectroscopy of Oxy-Picket Fence Porphyrin: Experimental Insight into FeāO<sub>2</sub> Bonding
The electronic structure of the FeāO<sub>2</sub> center
in oxy-hemoglobin and oxy-myoglobin is a long-standing issue in the
field of bioinorganic chemistry. Spectroscopic studies have been complicated
by the highly delocalized nature of the porphyrin, and calculations
require interpretation of multideterminant wave functions for a highly
covalent metal site. Here, iron L-edge X-ray absorption spectroscopy,
interpreted using a valence bond configuration interaction multiplet
model, is applied to directly probe the electronic structure of the
iron in the biomimetic FeāO<sub>2</sub> heme complex [FeĀ(pfp)Ā(1āMeIm)ĀO<sub>2</sub>] (pfp (āpicket fence porphyrinā) = <i>meso</i>-tetraĀ(Ī±,Ī±,Ī±,Ī±-<i>o</i>-pivalamidophenyl)Āporphyrin or TpivPP). This method allows separate
estimates of Ļ-donor, Ļ-donor, and Ļ-acceptor interactions
through ligand-to-metal charge transfer and metal-to-ligand charge
transfer mixing pathways. The L-edge spectrum of [FeĀ(pfp)Ā(1āMeIm)ĀO<sub>2</sub>] is further compared to those of [Fe<sup>II</sup>(pfp)Ā(1āMeIm)<sub>2</sub>], [Fe<sup>II</sup>(pfp)], and [Fe<sup>III</sup>(tpp)Ā(ImH)<sub>2</sub>]Cl (tpp = <i>meso</i>-tetraphenylporphyrin) which
have Fe<sup>II</sup> <i>S</i>Ā =Ā 0, Fe<sup>II</sup> <i>S</i>Ā =Ā 1, and Fe<sup>III</sup> <i>S</i>Ā =Ā 1/2 ground states, respectively. These serve as references
for the three possible contributions to the ground state of oxy-pfp.
The FeāO<sub>2</sub> pfp site is experimentally determined
to have both significant Ļ-donation and a strong Ļ-interaction
of the O<sub>2</sub> with the iron, with the latter having implications
with respect to the spin polarization of the ground state
LāEdge Xāray Absorption Spectroscopy and DFT Calculations on Cu<sub>2</sub>O<sub>2</sub> Species: Direct Electrophilic Aromatic Attack by Side-on Peroxo Bridged Dicopper(II) Complexes
The hydroxylation
of aromatic substrates catalyzed by coupled binuclear
copper enzymes has been observed with side-on-peroxo-dicopperĀ(II)
(<b>P</b>) and bis-Ī¼-oxo-dicopperĀ(III) (<b>O</b>) model complexes. The substrate-bound-<b>O</b> intermediate
in [CuĀ(II)<sub>2</sub>(DBED)<sub>2</sub>(O)<sub>2</sub>]<sup>2+</sup> (DBED = <i>N</i>,<i>N</i>ā²-di-<i>tert</i>-butyl-ethylenediamine) was shown to perform aromatic
hydroxylation. For the [CuĀ(II)<sub>2</sub>(NO<sub>2</sub>-XYL)Ā(O<sub>2</sub>)]<sup>2+</sup> complex, only a <b>P</b> species was
spectroscopically observed. However, it was not clear whether this
OāO bond cleaves to proceed through an <b>O</b>-type
structure along the reaction coordinate for hydroxylation of the aromatic
xylyl linker. Accurate evaluation of these reaction coordinates requires
reasonable quantitative descriptions of the electronic structures
of the <b>P</b> and <b>O</b> species. We have performed
Cu L-edge XAS on two well-characterized <b>P</b> and <b>O</b> species to experimentally quantify the Cu 3d character in their
ground state wave functions. The lower per-hole Cu character (40 Ā±
6%) corresponding to higher covalency in the <b>O</b> species
compared to the <b>P</b> species (52 Ā± 4%) reflects a stronger
bonding interaction of the bis-Ī¼-oxo core with the CuĀ(III) centers.
DFT calculations show that 10ā20% HartreeāFock (HF)
mixing for <b>P</b> and ā¼38% for <b>O</b> species
are required to reproduce the CuāO bonding; for the <b>P</b> species this HF mixing is also required for an antiferromagnetically
coupled description of the two CuĀ(II) centers. B3LYP (with 20% HF)
was, therefore, used to calculate the hydroxylation reaction coordinate
of <b>P</b> in [CuĀ(II)<sub>2</sub>(NO<sub>2</sub>-XYL)Ā(O<sub>2</sub>)]<sup>2+</sup>. These experimentally calibrated calculations
indicate that the electrophilic attack on the aromatic ring does not
involve formation of a CuĀ(III)<sub>2</sub>(O<sup>2ā</sup>)<sub>2</sub> species. Rather, there is direct electron donation from the
aromatic ring into the peroxo Ļ* orbital of the CuĀ(II)<sub>2</sub>(O<sub>2</sub><sup>2ā</sup>) species, leading to concerted
CāO bond formation with OāO bond cleavage. Thus, species <b>P</b> is capable of direct hydroxylation of aromatic substrates
without the intermediacy of an <b>O</b>-type species
Hydroxo-Bridged Dicopper(II,III) and -(III,III) Complexes: Models for Putative Intermediates in Oxidation Catalysis
A macrocyclic
ligand (L<sup>4ā</sup>) comprising two pyridineĀ(dicarboxamide)
donors was used to target reactive copper species relevant to proposed
intermediates in catalytic hydrocarbon oxidations by particulate methane
monooxygenase and heterogeneous zeolite systems. Treatment of LH<sub>4</sub> with base and CuĀ(OAc)<sub>2</sub>Ā·H<sub>2</sub>O yielded
(Me<sub>4</sub>N)<sub>2</sub>[L<sub>2</sub>Cu<sub>4</sub>(Ī¼<sub>4</sub>-O)] (<b>1</b>) or (Me<sub>4</sub>N)Ā[LCu<sub>2</sub>(Ī¼-OH)] (<b>2</b>), depending on conditions. Complex <b>2</b> was found to undergo two reversible 1-electron oxidations
via cyclic voltammetry and low-temperature chemical reactions. On
the basis of spectroscopy and theory, the oxidation products were
identified as novel hydroxo-bridged mixed-valent CuĀ(II)ĀCuĀ(III) and
symmetric CuĀ(III)<sub>2</sub> species, respectively, that provide
the first precedence for such moieties as oxidation catalysis intermediates
A Six-Coordinate Peroxynitrite Low-Spin Iron(III) Porphyrinate ComplexīøThe Product of the Reaction of Nitrogen Monoxide (Ā·NO<sub>(g)</sub>) with a Ferric-Superoxide Species
Peroxynitrite
(<sup>ā</sup>OONī»O, PN) is a reactive
nitrogen species (RNS) which can effect deleterious nitrative or oxidative
(bio)Āchemistry. It may derive from reaction of superoxide anion (O<sub>2</sub><sup>ā¢ā</sup>) with nitric oxide (Ā·NO)
and has been suggested to form an as-yet unobserved bound heme-iron-PN
intermediate in the catalytic cycle of nitric oxide dioxygenase (NOD)
enzymes, which facilitate a Ā·NO homeostatic process, i.e., its
oxidation to the nitrate anion. Here, a discrete six-coordinate low-spin
porphyrinate-Fe<sup>III</sup> complex [(P<sup>Im</sup>)ĀFe<sup>III</sup>(<sup>ā</sup>OONī»O)] (<b>3</b>) (P<sup>Im</sup>; a porphyrin moiety with a covalently tethered imidazole axial ābaseā
donor ligand) has been identified and characterized by various spectroscopies
(UVāvis, NMR, EPR, XAS, resonance Raman) and DFT calculations,
following its formation at ā80 Ā°C by addition of Ā·NO<sub>(g)</sub> to the heme-superoxo species, [(P<sup>Im</sup>)ĀFe<sup>III</sup>(O<sub>2</sub><sup>ā¢ā</sup>)] (<b>2</b>). DFT
calculations confirm that <b>3</b> is a six-coordinate low-spin
species with the PN ligand coordinated to iron via its terminal peroxidic
anionic O atom with the overall geometry being in a <i>cis</i>-configuration. Complex <b>3</b> thermally transforms to its
isomeric low-spin nitrato form [(P<sup>Im</sup>)ĀFe<sup>III</sup>(NO<sub>3</sub><sup>ā</sup>)] (<b>4a</b>). While previous (bio)Āchemical
studies show that phenolic substrates undergo nitration in the presence
of PN or PN-metal complexes, in the present system, addition of 2,4-di-<i>tert</i>-butylphenol (<sup>2,4</sup>DTBP) to complex <b>3</b> does not lead to nitrated phenol; the nitrate complex <b>4a</b> still forms. DFT calculations reveal that the phenolic H atom approaches
the terminal PN O atom (farthest from the metal center and ring core),
effecting OāO cleavage, giving nitrogen dioxide (Ā·NO<sub>2</sub>) plus a ferryl compound [(P<sup>Im</sup>)ĀFe<sup>IV</sup>ī»O]
(<b>7</b>); this rebounds to give [(P<sup>Im</sup>)ĀFe<sup>III</sup>(NO<sub>3</sub><sup>ā</sup>)] (<b>4a</b>).The generation
and characterization of the long sought after ferriheme peroxynitrite
complex has been accomplished