Spectroscopic and electronic structure studies of a dimethyl sulfoxide reductase catalytic intermediate: implications for electron- and atom-transfer reactivity

The electronic structure of a genuine paramagnetic des-oxo Mo(V) catalytic intermediate in the reaction of dimethyl sulfoxide reductase (DMSOR) with (CH(3))(3)NO has been probed by electron paramagnetic resonance (EPR), electronic absorption, and magnetic circular dichroism (MCD) spectroscopies. EPR spectroscopy reveals rhombic g- and A-tensors that indicate a low-symmetry geometry for this intermediate and a singly occupied molecular orbital that is dominantly metal centered. The excited-state spectroscopic data were interpreted in the context of electronic structure calculations, and this has resulted in a full assignment of the observed MCD and electronic absorption bands, a detailed understanding of the metal-ligand bonding scheme, and an evaluation of the Mo(V) coordination geometry and Mo(V)-S(dithiolene) covalency as it pertains to the stability of the intermediate and electron-transfer regeneration. Finally, the relationship between des-oxo Mo(V) and des-oxo Mo(IV) geometric and electronic structures is discussed relative to the reaction coordinate in members of the DMSOR enzyme family.     

Rapid-freeze-quench magnetic circular dichroism of intermediate X in ribonucleotide reductase: new structural insight

To elucidate the electronic structure of intermediate X in the oxygen activation reaction of the R2 subunit of ribonucleotide reductase, a protocol has been developed to perform magnetic circular dichroism (MCD) on a rapid-freeze-quench, strain free optical sample. RFQ-MCD data have been collected on intermediate X in the double mutant of R2, Y122/Y356F. While X has been reported to exhibit a broad absorption band at 365 nm, there are at least 10 electronic transitions observed at low-temperature MCD. From C0/D0 ratios, the transitions of X can be divided into three regions: 16 000-22 000 cm-1 region involving spin-allowed ligand field transitions of the Fe(IV), 23 000-24 000 cm-1 region of spin-forbidden, spin-flip transitions on the Fe(IV), and the charge transfer (CT) region from 26 000 to 32 000 cm-1. The C0/D0 ratios from d --> d and CT transitions strongly support significant Fe(IV) character coupled into the paramagnetic center. Ligand field (spin-allowed d --> d region) analysis allows the bis-mu-oxo and mu-oxo plus other monoanionic bridge possibilities for the structure of intermediate X to be distinguished, providing new insight into the molecular mechanism of the cluster formation in R2.     

Active site structure of class I ribonucleotide reductase intermediate X: a density functional theory analysis of structure, energetics, and spectroscopy

Several models for the active site structure of class I ribonucleotide reductase (RNR) intermediate X have been studied in the work described in this paper, using broken-symmetry density functional theory (DFT) incorporated with the conductor-like screening (COSMO) solvation model. The calculated properties, including geometries, spin states, 57Fe, 1H, and 17O hyperfine tensors, M?ssbauer isomer shifts, and quadrupole splittings, and the estimation of the Fe(IV) d-d transition energies have been compared with the available experimental values. On the basis of the detailed analysis and comparisons, we propose a definite form for the active site structure of class I RNR intermediate X, which contains an Fe1(III)Fe2(IV) center (where Fe1 is the iron site closer to Tyr122, and the two iron sites are high-spin antiferromagnetically coupled to give a total 1/2 net spin), two mu-oxo bridges, one terminal water which binds to Fe1(III) and also H-bonds to both side chains of Asp84 and Glu238, and one bidentate carboxylate group from the side chain of Glu115.     

Spectroscopic observation and structure of CS2 dimer

Infrared spectra of the CS(2) dimer are observed in the region of the CS(2) ν(3) fundamental band (～1535 cm(-1)) using a tunable diode laser spectrometer. The weakly bound complex is formed in a pulsed supersonic slit-jet expansion of a dilute gas mixture of carbon disulfide in helium. Contrary to the planar slipped-parallel geometry previously observed for (CO(2))(2), (N(2)O)(2), and (OCS)(2), the CS(2) dimer exhibits a cross-shaped structure with D(2d) symmetry. Two bands were observed and analyzed: the fundamental (C-S asymmetric stretch) and a combination involving this mode plus an intermolecular vibration. In both cases, the rotational structure corresponds to a perpendicular (ΔK = ±1) band of a symmetric rotor molecule. The intermolecular center of mass separation (C-C distance) is determined to be 3.539(7) A?. Thanks to symmetry, this is the only parameter required to characterize the structure, if the monomer geometry is assumed to remain unchanged in the dimer. From the band centers of the fundamental and combination band an intermolecular frequency of 10.96 cm(-1) is obtained, which we assign as the torsional bending mode. This constitutes the first high resolution spectroscopic investigation of CS(2) dimer.     

Electronic and spectroscopic studies of the non-heme reduced binuclear iron sites of two ribonucleotide reductase variants: comparison to reduced methane monooxygenase and contributions to O2 reactivity

Circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature variable-field (VTVH) MCD have been used to probe the biferrous active site of two variants of ribonucleotide reductase. The aspartate to glutamate substitution (R2-D84E) at the binuclear iron site modifies the endogenous ligand set of ribonucleotide reductase to match that of the binuclear center in the hydroxylase component of methane monooxygenase (MMOH). The crystal structure of chemically reduced R2-D84E suggests that the active-site structure parallels that of MMOH. However, CD, MCD, and VTVH MCD data combined with spin-Hamiltonian analysis of reduced R2-D84E indicate a different coordination environment relative to reduced MMOH, with no mu-(1,1)(eta(1),eta(2)) carboxylate bridge. To further understand the variations in geometry of the active site, which lead to differences in reactivity, density functional theory (DFT) calculations have been carried out to identify active-site structures for R2-wt and R2-D84E consistent with these spectroscopic data. The effects of varying the ligand set, positions of bound and free waters, and additional protein constraints on the geometry and energy of the binuclear site of both R2-wt and variant R2s are also explored to identify the contributions to their structural differences and their relation to reduced MMOH.     

Spectroscopic, electronic structure and natural bond orbital analysis of o-fluoronitrobenzene and p-fluoronitrobenzene: a comparative study

Experimental FTIR, FT-Raman and FT-NMR spectroscopic studies of o-fluoronitrobenzene and p-fluoronitrobenzene have been carried out. A detailed quantum chemical calculations have been performed using DFT/B3LYP method with 6-311++G** and 6-31G** basis sets. Complete vibrational analyses of the compounds were performed. The temperature dependence of thermodynamic properties has been analysed. The atomic charges, electronic exchange interaction and charge delocalisation of the molecule have been performed by natural bond orbital (NBO) analysis. Molecular electrostatic surface potential (MESP), total electron density distribution and frontier molecular orbitals (FMOs) are constructed at B3LYP/6-311++G** level to understand the electronic properties. The charge density distribution and site of chemical reactivity of the molecules have been obtained by mapping electron density isosurface with electrostatic potential surfaces (ESP). The electronic properties, HOMO and LUMO energies were measured by time-dependent TD-DFT approach. (1)H and (13)C NMR spectra were recorded and (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were calculated. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecules in chloroform solvent and in gas phase were calculated by using the Gauge-Independent Atomic Orbital (GIAO) method and are found to be in good agreement with experimental values. The theoretical parameters obtained at B3LYP levels have been compared with the experimental values.     

PELDOR study on the tyrosyl radicals in the R2 protein of mouse ribonucleotide reductase

Pulse electron-electron double resonance (PELDOR) has been employed to measure the distance between the putative tyrosyl radicals in the two halves of the R2 subunit from mouse ribonucleotide reductase. The results provide experimental evidence that the active, tyrosyl radical containing mouse R2 subunit forms a homodimeric form in solution. The distance between the two tyrosyl radicals present in the dimer was determined to be 3.25 +/- 0.05 nm.     

Rational reprogramming of the R2 subunit of Escherichia coli ribonucleotide reductase into a self-hydroxylating monooxygenase.

The outcome of O2 activation at the diiron(II) cluster in the R2 subunit of Escherichia coli (class I) ribonucleotide reductase has been rationally altered from the normal tyrosyl radical (Y122*) production to self-hydroxylation of a phenylalanine side-chain by two amino acid substitutions that leave intact the (histidine)2-(carboxylate)4 ligand set characteristic of the diiron-carboxylate family. Iron ligand Asp (D) 84 was replaced with Glu (E), the amino acid found in the cognate position of the structurally similar diiron-carboxylate protein, methane monooxygenase hydroxylase (MMOH). We previously showed that this substitution allows accumulation of a mu-1,2-peroxodiiron(III) intermediate, which does not accumulate in the wild-type (wt) protein and is probably a structural homologue of intermediate P (H(peroxo)) in O2 activation by MMOH. In addition, the near-surface residue Trp (W) 48 was replaced with Phe (F), blocking transfer of the "extra" electron that occurs in wt R2 during formation of the formally Fe(III)Fe(IV) cluster X. Decay of the mu-1,2-peroxodiiron(III) complex in R2-W48F/D84E gives an initial brown product, which contains very little Y122* and which converts very slowly (t1/2 approximately 7 h) upon incubation at 0 degrees C to an intensely purple final product. X-ray crystallographic analysis of the purple product indicates that F208 has undergone epsilon-hydroxylation and the resulting phenol has shifted significantly to become a ligand to Fe2 of the diiron cluster. Resonance Raman (RR) spectra of the purple product generated with 16O2 or 18O2 show appropriate isotopic sensitivity in bands assigned to O-phenyl and Fe-O-phenyl vibrational modes, confirming that the oxygen of the Fe(III)-phenolate species is derived from O2. Chemical analysis, experiments involving interception of the hydroxylating intermediate with exogenous reductant, and M?ssbauer and EXAFS characterization of the brown and purple species establish that F208 hydroxylation occurs during decay of the peroxo complex and formation of the initial brown product. The slow transition to the purple Fe(III)-phenolate species is ascribed to a ligand rearrangement in which mu-O2- is lost and the F208-derived phenolate coordinates. The reprogramming to F208 monooxygenase requires both amino acid substitutions, as very little epsilon-hydroxyphenylalanine is formed and pathways leading to Y122* formation predominate in both R2-D84E and R2-W48F.     

2,3-difluorotyrosine at position 356 of ribonucleotide reductase R2: a probe of long-range proton-coupled electron transfer

Escherichia coli class I ribonucleotide reductase catalyzes the conversion of ribonucleotides to deoxyribonucleotides and consists of two subunits: R1 and R2. R1 possesses the active site, while R2 harbors the essential diferric-tyrosyl radical (Y*) cofactor. The Y* on R2 is proposed to generate a transient thiyl radical on R1, 35 A distant, through amino acid radical intermediates. To study the putative long-range proton-coupled electron transfer (PCET), R2 (375 residues) was prepared semisynthetically using intein technology. Y356, a putative intermediate in the pathway, was replaced with 2,3-difluorotyrosine (F2Y, pKa = 7.8). pH rate profiles (pH 6.5-9.0) of wild-type and F2Y-R2 were very similar. Thus, a proton can be lost from the putative PCET pathway without affecting nucleotide reduction. The current model involving H* transfer is thus unlikely.     

Spectroscopic and computational studies of the de novo designed protein DF2t: correlation to the biferrous active site of ribonucleotide reductase and factors that affect O2 reactivity

DF2t, a de novo designed protein that mimics the active-site structure of many non-heme biferrous enzymes, has been studied using a combination of circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature variable-field (VTVH) MCD. The active site of DF2t is found to have one five-coordinate iron and one four-coordinate iron, which are weakly antiferromagnetically coupled through a mu-1,3 carboxylate bridge. These results bear a strong resemblance to the spectra of Escherichia coli ribonucleotide reductase (R2), and density functional theory calculations were conducted on the W48F/D84E R2 mutant in order to determine the energetics of formation of a monodentate end-on-bound O2 to one iron in the binuclear site. The mu-1,3 carboxylate bridges found in O2-activating enzymes lack efficient superexchange pathways for the second electron transfer (i.e., the OH/oxo bridge in hemerythrin), and simulations of the binding of O2 in a monodentate end-on manner revealed that the bridging carboxylate ligands do not appear capable of transferring an electron to O2 from the remote Fe. Comparison of the results from previous studies of the mu-1,2 biferric-peroxo structure, which bridges both irons, finds that the end-on superoxide mixed-valent species is considerably higher in energy than the bridging peroxo-diferric species. Thus, one of the differences between O2-activating and O2-binding proteins appears to be the ability of O2 to bridge both Fe centers to generate a peroxo intermediate capable of further reactivity.     

Pulsed ELDOR spectroscopy measures the distance between the two tyrosyl dadicals in the R2 subunit of the E. coli ribonucleotide reductase

Escherichia coli ribonucleotide reductase (RNR) catalyzes the conversion of nucleoside diphosphates (NDPs) to deoxynucleoside diphosphates (dNDPs). This RNR is composed of two homodimeric subunits: R1 and R2. R1 binds the NDPs in the active site, and R2 harbors the essential di-iron tyrosyl radical (Y*) cofactor. In this paper, we used PELDOR, a method that detects weak electron-electron dipolar coupling, to make the first direct measurement of the distance between the two Y*'s on each monomer of R2. In the crystal structure of R2, the Y*'s are reduced to tyrosines, and consequently R2 is inactive. In R2, where the Y*'s assume a well-defined geometry with respect to the protein backbone, the PELDOR method allows measurement of a distance of 33.1 +/- 0.2 A that compares favorably to the distance (32.4 A) between the center of mass of the spin density distribution of each Y* on each R2 monomer from the structure. The experiments provide the first direct experimental evidence for two Y*'s in a single R2 in solution.     

Spectroscopic investigation of the electronic structure of 1,2-naphthoquinone-2-diazides

Theoretical and Experimental Chemistry -     

The electronic structure of the HCN dimer and trimer

The electronic structure and energy of dimerization and trimerization of HCN are computed with an STO-3G basis and the results found to be in good agreement with the experimental E. Unlike CNDO/2, this small ab initio basis predicts the correct geometry for the dimer of hydrogen cyanide. The charge redistribution effects found in this H-bond involving a C-H proton donor and sp hybridized acceptor are similar to those found in previous H-bonded studies.     

Spectroscopic studies of the Met182Thr mutant of nitrite reductase: role of the axial ligand in the geometric and electronic structure of blue and green copper sites

A combination of spectroscopic methods and density functional calculations has been used to describe the electronic structure of the axial mutant (Met182Thr) of Rhodobacter sphaeroides nitrite reductase in which the axial methionine has been changed to a threonine. This mutation results in a dramatic change in the geometric and electronic structure of the copper site. The electronic absorption data imply that the type 1 site in the mutant is like a typical blue copper site in contrast to the wild-type site, which is green. Similar ligand field strength in the mutant and the wild type (from MCD spectra) explains the similar EPR parameters for very different electronic structures. Resonance Raman shows that the Cu-S(Cys) bond is stronger in the mutant relative to the wild type. From a combination of absorption, CD, MCD, and EPR data, the loss of the strong axial thioether (present in the wild-type site) results in an increase of the equatorial thiolate-Cu interaction and the site becomes less tetragonal. Spectroscopically calibrated density functional calculations were used to provide additional insight into the role of the axial ligand. The calculations reproduce well the experimental ground-state bonding and the changes in going from a green to a blue site along this coupled distortion coordinate. Geometry optimizations at the weak and strong axial ligand limits show that the bonding of the axial thioether is the key factor in determining the structure of the ground state. A comparison of plastocyanin (blue), wild-type nitrite reductase (green), and the Met182Thr mutant (blue) sites enables evaluation of the role of the axial ligand in the geometric and electronic structure of type 1 copper sites, which can affect the electron-transfer properties of these sites.