Hydrogen bond geometries from electron paramagnetic resonance and electron-nuclear double resonance parameters: density functional study of quinone radical anion-solvent interactions

Density functional theory was used to study the impact of hydrogen bonding on the p-benzosemiquinone radical anion BQ(*-) in coordination with water or alcohol molecules. After complete geometry optimizations, (1)H, (13)C, and (17)O hyperfine as well as (2)H nuclear quadrupole coupling constants and the g-tensor were computed. The suitability of different model systems with one, two, four, and 20 water molecules was tested; best agreement between theory and experiment could be obtained for the largest model system. Q-band pulse (2)H electron-nuclear double resonance (ENDOR) experiments were performed on BQ(*-) in D(2)O. They compare very well with the spectra simulated by use of the theoretical values from density functional theory. For BQ(*-) in coordination with four water or alcohol molecules, rather similar hydrogen-bond lengths between 1.75 and 1.78 A were calculated. Thus, the computed electron paramagnetic resonance (EPR) parameters are hardly distinguishable for the different solvents, in agreement with experimental findings. Furthermore, the distance dependence of the EPR parameters on the hydrogen-bond length was studied. The nuclear quadrupole and the dipolar hyperfine coupling constants of the bridging hydrogens show the expected dependencies on the H-bond length R(O.H). A correlation was obtained for the g-tensor. It is shown that the point-dipole model is suitable for the estimation of hydrogen-bond lengths from anisotropic hyperfine coupling constants of the bridging (1)H nuclei for H-bond lengths larger than approximately 1.7 A. Furthermore, the estimation of H-bond lengths from (2)H nuclear quadrupole coupling constants of bridging deuterium nuclei by empirical relations is discussed.     

Identification of the nitrogen donor hydrogen bonded with the semiquinone at the Q(H) site of the cytochrome bo3 from Escherichia coli

The selective (15)N isotope labeling was used for the identification of the nitrogen involved in a hydrogen bond formation with the semiquinone in the high-affinity Q(H) site in the cytochrome bo(3) ubiquinol oxidase. This nitrogen produces dominating contribution to X-Band (14)N ESEEM spectra. The 2D ESEEM (HYSCORE) experiments with the Q(H) site SQ in the series of selectively (15)N labeled bo(3) oxidase proteins have directly identified the N(epsilon) of R71 as an H-bond donor. In addition, selective (15)N labeling has allowed us for the first time to determine weak hyperfine couplings with the side-chain nitrogens from all residues around the SQ. Those are reflecting a distribution of the unpaired spin density over the protein in the SQ state of the quinone processing site.     

A density functional theory investigation of Fe-N-O bonding in heme proteins and model systems

We report the results of a series of density functional theory (DFT) calculations of the M?ssbauer quadrupole splittings and isomer shifts in NO heme model compounds, together with the results of calculations of the M?ssbauer quadrupole splittings, isomer shifts, and electron paramagnetic resonance hyperfine coupling constants in a model Fe(II)(NO)(imidazole) complex as a function of Fe-NO bond length and Fe-N-O bond angle. The results of the M?ssbauer quadrupole splitting and isomer shift calculations on the NO heme model compounds show good accord between theory and experiment, with the largest errors being observed for structures having the largest crystallographic R(1) values. The results of the property surface calculations were then used to calculate Fe-NO bond length and Fe-N-O bond angle probability surfaces (Z-surfaces) for a nitrosyl hemoglobin, using, in addition, an energy filter. The results obtained yielded a most probable Fe-NO bond length (r) of 1.79 A and an Fe-N-O bond angle (beta) of 136 degrees -137 degrees. This bond length is somewhat longer than those observed in most model compounds but may be due, at least in part, to hydrogen bond formation with the distal His residue. Bond elongation was also observed in a geometry optimized Fe(II)(NO)(imidazole) complex hydrogen bonded to an imidazole residue, in which we find r = 1.76-1.78 A and beta = 137 degrees -138 degrees. The computed bond angles are close to the canonical approximately 140 degrees value found in most model systems. Highly bent Fe-N-O bond angles or very long Fe-NO bond lengths seem unlikely to occur in proteins, due to their high energies. We also investigated the molecular orbitals and spin densities in each of the six coordinate systems investigated and found the orbitals and spin densities to be generally similar those described previously for five coordinate systems. Taken together, these results show that M?ssbauer quadrupole splittings and isomer shifts, in addition to electron paramagnetic resonance hyperfine coupling constants, can now be calculated for nitrosyl heme systems with relatively good accuracy and that the results so obtained can be used to determine Fe-N-O geometries in metalloproteins. The Z-surface approach is thus applicable to both diamagnetic (CO) and paramagnetic (NO) heme proteins with in both cases the metal-ligand binding geometries found in the proteins being very close to those seen in model systems.     

Molecular structure of substituted phenylamine alpha-OMe- and alpha-OH-p-benzoquinone derivatives. Synthesis and correlation of spectroscopic, electrochemical, and theoretical parameters.

Thirteen C(6) para-substituted anilinebenzoquinones derived from perezone (PZ) (2-(1,5-dimethyl-4-hexenyl)-3-hydroxy-5-methyl-1,4-benzoquinone) were prepared to analyze the effect of the substituents on quinone electronic properties. The effect of a hydrogen bond between the alpha-hydroxy and carbonyl C(4)-O(4) groups was determined in perezone derivatives by substituting electron-donor and electron-acceptor groups such as -OMe, -Me, -Br, and -CN and comparing the -OH (APZs) and -OMe (APZms) derivatives. Reduction potentials of these compounds were measured using cyclic voltammetry in anhydrous acetonitrile. The typical behavior of quinones, with or without alpha-phenolic protons, in an aprotic medium was not observed for APZs due to the presence of coupled, self-protonation reactions. The self-protonation process gives rise to an initial wave, corresponding to the irreversible reduction reaction of quinone (HQ) to hydroquinone (HQH(2)), and to a second electron transfer, attributed to the reversible reduction of perezonate (Q(-)) formed during the self-protonation process. This reaction is favored by the acidity of the alpha-OH located at the quinone ring. To control the coupled chemical reaction, we considered both methylation of the -OH group (APZms) and addition of a strong base, tetramethylammonium phenolate (Me(4)N(+)C(6)H(5)O(-)), to completely deprotonate the APZs. Methylation led to recovery of reversible, bi-electronic behavior (Q/Q(*)(-) and Q(*)(-)/Q(2)(-)), indicating the nonacidic properties of the NH group. The addition of a strong base resulted in reduction of perezonate (Q(-)) obtained from the acid-base reaction of APZs with Me(4)N(+)C(6)H(5)O(-) to produce the dianion radical (Q(*)(2)(-)). Although the nitrogen atom interferes with direct conjugation between both rings by binding the quinone with the para-substituted ring, the UV-vis spectra of these compounds showed the existence of intramolecular electronic transfer from the respective aniline to the quinone moiety. (13)C NMR chemical shifts of the quinone atoms provided additional evidence for this electron transfer. These findings were also supported by linear variation in cathodic peak potentials (E(pc)) vs Hammett sigma(p) constants associated with the different electrochemical transformations: Q/Q(*)(-), Q(*)(-)/Q(2)(-) for APZms or HQ/HQH(2) and Q(-)/Q(*)(2)(-) for APZs. The electronic properties of model anilinebenzoquinones were determined at a B3LYP/6-31G(d,p) level of theory within the framework of the density functional theory. Our theoretical calculations predicted that all the compounds are floppy molecules with a low rotational C-N barrier, in which the degree of conjugation of the lone nitrogen pair with the quinone system depends on the magnitude of the electronic effect of the substituents of the aniline ring. Natural charges show that C(1) is more positive than C(4) although the LUMO orbital is located at C(4). Hence, if the natural charge distribution in the molecule controls the first electron addition, this should occur at carbon atom C(1). If the process is controlled by the LUMO orbitals, however, electron addition would first occur at C(4). For the APZms series susceptibility of the first reduction wave to the substitution effect (rho(pi) = 147 mV) is lower than that of the second reduction wave (rho(pi) = 156 mV). Thus, the first, one-electron transfer in the quinone system is controlled by the natural charge distribution of the molecule and therefore takes place at C(1).     

ENDOR investigation of the liganding environment of mixed-spin ferric cytochrome c'

The electronic structure of the 5-coordinate quantum-mechanically mixed-spin (sextet-quartet) heme center in cytochrome c' was investigated by electron nuclear double resonance (ENDOR), a technique not previously applied to this mixed-spin system. Cytochrome c' was obtained from overexpressing variants of Rhodobacter sphaeroides 2.4.3. ENDOR for this study was done at the g(//) = 2.00 extremum where single-crystal-like, well-resolved spectra prevail. The heme meso protons of cytochrome c' showed a contact interaction that implied spin delocalization arising from the heme (d(z)(2)) orbital enhanced by iron out-of-planarity. An exchangeable proton ENDOR feature appeared from the proximal His123 Ndelta hydrogen. This Ndelta hydrogen, which crystallographically has no hydrogen-bonding partner and thus belongs to a neutral imidazole, showed a larger hyperfine coupling than the corresponding hydrogen-bonded Ndelta proton from metmyoglobin. The unique residue Phe14 occludes binding of a sixth ligand in cytochrome c', and ENDOR from a proton of the functionally important Phe14 ring, approximately 3.3 A away from the heme iron, was detected. ENDOR of the nitrogen ligand hyperfine structure is a direct probe into the sigma-antibonding (d(z)(2)) and (d(x)(2)-d(y)(2)) orbitals whose energies alter the relative stability and admixture of sextet and quartet states and whose electronic details were thus elucidated. ENDOR frequencies showed for cytochrome c' larger hyperfine couplings to the histidine nitrogen and smaller hyperfine couplings to the heme nitrogens than for high-spin ferric hemes. Both of these findings followed from the mixed-spin ground state, which has less (d(x)(2)-d(y)(2)) character than have fully high-spin ferric heme systems.     

(TAML)FeIV O complex in aqueous solution: synthesis and spectroscopic and computational characterization

Recently, we reported the characterization of the S = (1)/ 2 complex [Fe (V)(O)B*] (-), where B* belongs to a family of tetraamido macrocyclic ligands (TAMLs) whose iron complexes activate peroxides for environmentally useful applications. The corresponding one-electron reduced species, [Fe (IV)(O)B*] (2-) ( 2), has now been prepared in >95% yield in aqueous solution at pH > 12 by oxidation of [Fe (III)(H 2O)B*] (-) ( 1), with tert-butyl hydroperoxide. At room temperature, the monomeric species 2 is in a reversible, pH-dependent equilibrium with dimeric species [B*Fe (IV)-O-Fe (IV)B*] (2-) ( 3), with a p K a near 10. In zero field, the M?ssbauer spectrum of 2 exhibits a quadrupole doublet with Delta E Q = 3.95(3) mm/s and delta = -0.19(2) mm/s, parameters consistent with a S = 1 Fe (IV) state. Studies in applied magnetic fields yielded the zero-field splitting parameter D = 24(3) cm (-1) together with the magnetic hyperfine tensor A/ g nbeta n = (-27, -27, +2) T. Fe K-edge EXAFS analysis of 2 shows a scatterer at 1.69 (2) A, a distance consistent with a Fe (IV)O bond. DFT calculations for [Fe (IV)(O)B*] (2-) reproduce the experimental data quite well. Further significant improvement was achieved by introducing hydrogen bonding of the axial oxygen with two solvent-water molecules. It is shown, using DFT, that the (57)Fe hyperfine parameters of complex 2 give evidence for strong electron donation from B* to iron.     

Proton uptake of rhodobacter capsulatus reaction center mutants modified in the primary quinone environment

Flash-induced absorbance spectroscopy was used to analyze the proton uptake and electron transfer properties of photosynthetic reaction centers (RC) of Rhodobacter capsulatus that have been genetically modified near the primary quinone electron acceptor (Q(A)). M246Ala and M247Ala, which are symmetry-related to the positions of two acidic groups, L212Glu and L213Asp, in the secondary quinone electron acceptor (QB) protein environment, have been mutated to Glu and Asp, respectively. The pH dependence of the stoichiometry of proton uptake upon formation of the P+Q(A)- (H+/P+Q(A)-) and PQ(A) (H+/Q(A)-) (P is the primary electron donor, a noncovalently linked bacteriochlorophyll dimer) states have been measured in the M246Ala --> Glu and the M247Ala --> Asp mutant RC, in the M246Ala-M247Ala --> Glu-Asp double mutant and in the wild type (WT). Our results show that the introduction of an acidic group (Glu or Asp) in the QA protein region induces notable additional proton uptake over a large pH region (approximately 6-9), which reflects a delocalized response of the protein to the formation of Q(A)-. This may indicate the existence of a widely spread proton reservoir in the cytoplasmic region of the protein. Interestingly, the pH titration curves of the proton release caused by the formation of P+ (H+/P+: difference between H+/P+Q(A)- and H+/PQ(A)- curves) are nearly superimposable in the WT and the M246Ala --> Glu mutant RC, but substantial additional proton release is detected between pH 7 and 9 in the M247Ala --> Asp mutant RC. This effect can be accounted for by an increased proton release by the P+ environment in the M247Ala --> Asp mutant. The M247Ala --> Asp mutation reveals the existence of an energetic and conformational coupling between donor and acceptor sides of the RC at a distance of nearly 30A.     

Electronic structure of binuclear mixed valence copper azacryptates derived from integrated advanced EPR and DFT calculations

Binuclear, mixed valence copper complexes with a [Cu(+1)(.5), Cu(+1)(.5)] redox state and S = (1)/(2) can be stabilized with rigid azacryptand ligands. In this system the unpaired electron is delocalized equally over the two copper ions, and it is one of the very few synthetic models for the electron mediating Cu(A) site of nitrous oxide reductase and cytochrome c oxidase. The spatial and electronic structures of the copper complex in frozen solution were obtained from the magnetic interactions, namely the g-tensor and the (63,65)Cu, (14)N, (2)H, and (1)H hyperfine couplings, in combination with density functional theory (DFT) calculations. The magnetic interactions were determined from continuous wave (CW) electron paramagnetic resonance (EPR), pulsed electron nuclear double resonance (ENDOR), two-dimensional TRIPLE, and hyperfine sublevel correlation spectroscopy (HYSCORE) carried out at W-band or/and X-band frequencies. The DFT calculated g and Cu hyperfine values were in good agreement with the experimental values showing that the structure in solution is indeed close to that of the optimized structure. Then, the DFT calculated hyperfine parameters were used as guidelines and starting points in the simulations of the various experimental ENDOR spectra. A satisfactory agreement with the experimental results was obtained for the (14)N hyperfine and quadrupole interactions. For (1)H the DFT calculations gave good predictions for the hyperfine tensor orientations and signs, and they were also successful in reproducing trends in the magnitude of the various proton hyperfine couplings. These, in turn, were very useful for ENDOR signals assignments and served as constraints on the simulation parameters.     

Control of quinone redox potentials in photosystem II: Electron transfer and photoprotection

In O(2)-evolving complex Photosystem II (PSII), an unimpeded transfer of electrons from the primary quinone (Q(A)) to the secondary quinone (Q(B)) is essential for the efficiency of photosynthesis. Recent PSII crystal structures revealed the protein environment of the Q(A/B) binding sites. We calculated the plastoquinone (Q(A/B)) redox potentials (E(m)) for one-electron reduction with a full account of the PSII protein environment. We found two different H-bond patterns involving Q(A) and D2-Thr217, resulting in an upshift of E(m)(Q(A)) by 100 mV if the H bond between Q(A) and Thr is present. The formation of this H bond to Q(A) may be the origin of a photoprotection mechanism, which is under debate. At the Q(B) side, the formation of a H bond between D2-Ser264 and Q(B) depends on the protonation state of D1-His252. Q(B) adopts the high-potential form if the H bond to Ser is present. Conservation of this residue and H-bond pattern for Q(B) sites among bacterial photosynthetic reaction centers (bRC) and PSII strongly indicates their essential requirement for electron transfer function.     

Evaluation of 27Al and 51V electric field gradients and the crystal structure for aluminum orthovanadate (AlVO4) by density functional theory calculations

Three sets of crystal-structure data reported for AlVO(4) from two powder-XRD studies and a density functional theory (DFT) investigation, employing the Vienna ab initio simulation package (VASP), have been examined and refined using the DFT structure-optimization scheme implemented in the WIEN2k software. The crystal structures are evaluated on the basis of (27)Al and (51)V quadrupole coupling parameters recently reported for AlVO(4), employing the corresponding electric-field gradient (EFG) tensor elements obtained from the DFT calculations. The DFT calculations provide a reliable assignment of the (27)Al/(51)V resonances from three distinct Al and three V environments to the specific crystallographic sites in the asymmetric unit for AlVO(4). An improved agreement between experimental quadrupole tensor elements and calculated EFG tensors is achieved after the DFT structure optimizations and consistent results are obtained using the three different structures as starting points. The improvement of the structural data is also supported by an evaluation of the Al-O and V-O bond lengths before and after DFT structure optimization. The (51)V nuclear quadrupole moment, |Q((51)V)| = 4.8 +/- 0.1 fm(2), derived from the present analysis, represents a value of higher accuracy than earlier reported Q((51)V) values. The origin of the (27)Al and (51)V EFGs are investigated by an evaluation of the orientations of the EFG tensors in the crystal frame and by an examination of the individual contributions from the valence electrons and the surrounding lattice. The latter investigation shows that the magnitude and orientation of the tensors are largely determined by the p-p((27)Al) and p-p, d-d((51)V) orbital contributions to the valence electrons, while the lattice part only gives a minor contribution for both nuclei.     

Hydrogen bond donating ability of meta and para hydroxy phenoxyl radicals

H-bond complexes between 3- or 4-OH phenoxyl radicals and various H-bond accepting molecules were investigated by experimental and computational methods. The H-bond donating ability (α(2)(H)) of 2,6-di-tert-butyl-4-hydroxyphenoxyl radical (1) was determined as 0.79 ± 0.05 by measuring, using EPR spectroscopy, the variations of the hyperfine splitting constants of 1 as a function of the acceptor concentrations. A computational approach, based on DFT calculations, was employed to estimate the α(2)(H) values for OH-substituted phenoxyl radicals that were not persistent enough to be studied by EPR spectroscopy. The α(2)(H) value calculated for the 2,6-di-methyl analogue of 1 was 0.76, in good agreement with EPR experiments. The α(2)(H) values for 2-methoxy-4-hydroxy (3), 4-hydroxy (4), 4,6-di-methyl-3-hydroxy (5) and 3-hydroxy (6) phenoxyl radicals were computed as 0.77, 0.84, 0.66 and 0.71, respectively, indicating that α(2)(H) values were dependent on the presence of electron donating substituents and on the relative positions of the -OH and -O˙ groups. By correlating the α(2)(H) values for 4 and 6 with their water and gas-phase acidities, an unexpected role of water in promoting proton dissociation from these radicals was evidenced.     

Hydrogen bonding and spin density distribution in the Qb semiquinone of bacterial reaction centers and comparison with the Qa site

In the photosynthetic reaction center from Rhodobacter sphaeroides, the primary (Q(A)) and secondary (Q(B)) electron acceptors are both ubiquinone-10, but with very different properties and functions. To investigate the protein environment that imparts these functional differences, we have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the Q(A) and Q(B) sites, using samples of (15)N-labeled reaction centers, with the native high spin Fe(2+) exchanged for diamagnetic Zn(2+), prepared in (1)H(2)O and (2)H(2)O solvent. The powder HYSCORE method is first validated against the orientation-selected Q-band ENDOR study of the Q(A) SQ by Flores et al. (Biophys. J.2007, 92, 671-682), with good agreement for two exchangeable protons with anisotropic hyperfine tensor components, T, both in the range 4.6-5.4 MHz. HYSCORE was then applied to the Q(B) SQ where we found proton lines corresponding to T ≈ 5.2, 3.7 MHz and T ≈ 1.9 MHz. Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a model of the Q(B) site, were used to assign the observed couplings to specific hydrogen bonding interactions with the Q(B) SQ. These calculations allow us to assign the T = 5.2 MHz proton to the His-L190 N(δ)H···O(4) (carbonyl) hydrogen bonding interaction. The T = 3.7 MHz spectral feature most likely results from hydrogen bonding interactions of O1 (carbonyl) with both Gly-L225 peptide NH and Ser-L223 hydroxyl OH, which possess calculated couplings very close to this value. The smaller 1.9 MHz coupling is assigned to a weakly bound peptide NH proton of Ile-L224. The calculations performed with this structural model of the Q(B) site show less asymmetric distribution of unpaired spin density over the SQ than seen for the Q(A) site, consistent with available experimental data for (13)C and (17)O carbonyl hyperfine couplings. The implications of these interactions for Q(B) function and comparisons with the Q(A) site are discussed.     

Metal ion-promoted intramolecular electron transfer in a ferrocene-naphthoquinone linked dyad. Continuous change in driving force and reorganization energy with metal ion concentration

Thermal intramolecular electron transfer from the ferrocene (Fc) to naphthoquinone (NQ) moiety occurs efficiently by the addition of metal triflates (M(n)()(+): Sc(OTf)(3), Y(OTf)(3), Eu(OTf)(3)) to an acetonitrile solution of a ferrocene-naphthoquinone (Fc-NQ) linked dyad with a flexible methylene and an amide spacer, although no electron transfer takes place in the absence of M(n)()(+). The resulting semiquinone radical anion (NQ(*)(-)) is stabilized by the strong binding of M(n)()(+) with one carbonyl oxygen of NQ(*)(-)( )()as well as hydrogen bonding between the amide proton and the other carbonyl oxygen of NQ(*)(-). The high stability of the Fc(+)()-NQ(*)(-)/M(n)()(+)() complex allows us to determine the driving force of electron transfer by the conventional electrochemical method. The one-electron reduction potential of the NQ moiety of Fc-NQ is shifted to a positive direction with increasing concentration of M(n)()(+), obeying the Nernst equation, whereas the one-electron oxidation potential of the Fc moiety remains the same. The driving force dependence of the observed rate constant (k(ET)) of M(n)()(+)-promoted intramolecular electron transfer is well evaluated in light of the Marcus theory of electron transfer. The driving force of electron transfer increases with increasing concentration of M(n)()(+) [M(n)()(+)], whereas the reorganization energy of electron transfer decreases with increasing [M(n)()(+)] from a large value which results from the strong binding between NQ(*)(-) and M(n)()(+).     

1H NMR study of the magnetic properties and electronic structure of the hydroxide complex of substrate-bound heme oxygenase from Neisseria meningitidis: influence of the axial water deprotonation on the distal H-bond network

The substrate and active site residues of the low-spin hydroxide complex of the protohemin complex of Neisseria meningitidis heme oxygenase (NmHO) have been assigned by saturation transfer between the hydroxide and previously characterized aquo complex. The available dipolar shifts allowed the quantitation of both the orientation and anisotropy of the paramagnetic susceptibility tensor. The resulting positive sign, and reduced magnitude of the axial anisotropy relative to the cyanide complex, dictate that the orbital ground state is the conventional "d(pi)" (d(2)(xy)(d(xz), d(yz))(3)); and not the unusual "d(xy)" (d(2)(xz)d(2)(yz)d(xy)) orbital ground state reported for the hydroxide complex of the homologous heme oxygenase (HO) from Pseudomonas aeruginosa (Caignan, G.; Deshmukh, R.; Zeng, Y.; Wilks, A.; Bunce, R. A.; Rivera, M. J. Am. Chem. Soc. 2003, 125, 11842-11852) and proposed as a signature of the HO distal cavity. The conservation of slow labile proton exchange with solvent from pH 7.0 to 10.8 confirms the extraordinary dynamic stability of NmHO complexes. Comparison of the diamagnetic contribution to the labile proton chemical shifts in the aquo and hydroxide complexes reveals strongly conserved bond strengths in the distal H-bond network, with the exception of the distal His53 N(epsilon)(1)H. The iron-ligated water is linked to His53 primarily by a pair of nonligated, ordered water molecules that transmit the conversion of the ligated H-bond donor (H(2)O) to a H-bond acceptor (OH(-)), thereby increasing the H-bond donor strength of the His53 side chain.     

How can a single second sphere amino acid substitution cause reduction midpoint potential changes of hundreds of millivolts?

The active site metal ion of superoxide dismutase (SOD) is reduced and reoxidized as it disproportionates superoxide to dioxygen and hydrogen peroxide. Thus, the reduction midpoint potential (Em) is a critical determinant of catalytic activity. In E. coli Fe-containing SOD (FeSOD), reduction of Fe3+ is accompanied by protonation of a coordinated OH-, to produce Fe2+ coordinated by H2O. The coordinated solvent's only contact with the protein beyond the active site is a conserved Gln residue. Mutation of this Gln to His or Glu resulted in elevation of the Em by 220 mV and more than 660 mV, respectively [Yikilmaz et al., Biochemistry 2006, 45, 1151-1161], despite the fact that overall protein structure was preserved, His is a chemically conservative replacement for Gln, and neutral Glu is isostructural and isoelectronic with Gln. Therefore, we have investigated several possible bases for the elevated Em's, including altered Fe electronic structure, altered active site electrostatics, altered H-bonding and altered redox-coupled proton transfer. Using EPR, MCD, and NMR spectroscopies, we find that the active site electronic structures of the two mutants resemble that of the WT enzyme, for both oxidation states, and Q69E-FeSOD's apparent deviation from WT-like Fe3+ coordination in the oxidized state can be explained by increased affinity for a small anion. Spontaneous coordination of an exogenous anion can only stabilize oxidized Q69E-Fe3+SOD and, therefore, cannot account for the increased Em of Q69E FeSOD. WT-like anion binding affinities and active site pK's indicate that His69 of Q69H-FeSOD is neutral in both oxidation states, like Gln69 of WT-FeSOD, whereas Glu69 appears to be neutral in the oxidized state but ionized in the reduced state of Q69E-FeSOD. A 1.1 A resolution crystal structure of Q69E-Fe2+SOD indicates that Glu69 accepts a strong H-bond from coordinated solvent in the reduced state, in contrast to the case in WT-FeSOD where Gln69 donates an H-bond. These data and DFT calculations lead to the proposal that the elevated Em of Q69E-FeSOD can be substantially explained by (1) relief from enforced H-bond donation in the reduced state, (2) Glu69's capacity to provide a proton for proton-coupled Fe3+ reduction, and (3) strong hydrogen bond acceptance in the reduced state, which stabilizes coordinated H2O. Our results thus support the hypothesis that the protein matrix can apply significant redox tuning via its influence over redox-coupled proton transfer and the energy associated with it.     

Spectroscopic and computational evaluation of the structure of the high-spin Fe(IV)-oxo intermediates in taurine: alpha-ketoglutarate dioxygenase from Escherichia coli and its His99Ala ligand variant

The Fe(II)- and alpha-ketoglutarate (alphaKG)-dependent dioxygenases activate O2 for cleavage of unactivated C-H bonds in their substrates. The key intermediate that abstracts hydrogen in the reaction of taurine:alphaKG dioxygenase (TauD), a member of this enzyme family, was recently characterized. The intermediate, denoted J, was shown to contain an iron(IV)-oxo unit. Other important structural features of J, such as the number, identity, and disposition of ligands in the Fe(IV) coordination sphere, are not yet understood. To probe these important structural features, a series of models for J with the Fe(IV) ion coordinated by the expected two imidazole (from His99 and His255), two carboxylate (succinate and Asp101), and oxo ligands have been generated by density functional theory (DFT) calculations, and spectroscopic parameters (M?ssbauer isomer shift, quadrupole splitting, and asymmetry parameter, 57Fe hyperfine coupling tensor, and zero field splitting parameters, D and E/D) have been calculated for each model. The calculated parameters of distorted octahedral models for J, in which one of the carboxylates serves as a monodentate ligand and the other as a bidentate ligand, and a trigonal bipyramidal model, in which both carboxylates serve as monodentate ligands, agree well with the experimental parameters, whereas the calculated parameters of a square pyramidal model, in which the oxo ligand is in the equatorial plane, are inconsistent with the data. Similar analysis of the Fe(IV) complex generated in the variant protein with His99, the residue that contributes the imidazole ligand cis to the oxo group, replaced by alanine suggests that the deleted imidazole is replaced by a water ligand. This work lends credence to the idea that the combination of M?ssbauer spectroscopy and DFT calculations can provide detailed structural information for reactive intermediates in the catalytic cycles of iron enzymes.     

Solution 1H NMR characterization of the distal H-bond network and the effective axial field in the resting-state, high-spin ferric, substrate-bound complex of heme oxygenase from N. meningitidis

The solution (1)H 1D and 2D NMR spectra of the high-spin ferric, resting-state, substrate-bound complex of heme oxygenase, HO, from the pathological bacterium N. meningitidis have been investigated to assess the prospects for definitive assignment of hyperfine shifted and relaxed residue protons and the interpretation of those shifts in terms of the anisotropy and orientation of the paramagnetic susceptibility tensor, chi. Appropriately tailored 1D/2D NMR data, together with analyses of paramagnetic relaxation and a preliminary estimate of the magnetic anisotropy, reveal a chi that is axially anisotropic and oriented along the Fe-His vector. Together with T(-)(2) dependence of the shifts, Deltachi(ax) yields a zero-field splitting constant, D = 9.1 cm(-)(1), which is expected to serve as a very sensitive probe of H-bond interactions between the iron-ligated water and a series of distal ordered water molecules implicated in the mechanism of HO action. The side chains, Gln49 and His53, involved in the stabilization of catalytically relevant water molecules, were found to exhibit orientations rotated by 180 degrees about the beta-gamma bonds in solution relative to those in the crystal. The implication of these reorientations on the details of the distal H-bond network is discussed. The H-bond donor strengths of Gln 49 and His53 were found to respond appropriately to H-bond donor (water) versus H-bond acceptor (cyanide) iron ligands. Very slow NH exchange for the N-terminal portion of the distal helix suggest that an intrinsically "unstable" distal helix may be valid only for the C-terminal portion.     

Proton transfer in hydrogen-bonded pyridine/acid systems: the role of higher aggregation

In this work the role of higher molecular aggregation in the proton transfer processes within hydrogen bond (H-bond) is investigated. The H-bonded complex consisting of 4-cyanopyridine (CyPy) with trichloroacetic acid (TCA) has been studied in the solutions of acetonitrile, carbon tetrachloride, chloroform and dichloroethane as solvent by FTIR spectroscopy and quantum chemical DFT calculations. In order to illustrate the effect of increasing H-bond strength FTIR investigations have also been performed on solutions of CyPy with H(2)O, acetic-, trifluoroacetic- and methanesulfonic acids. Proton states in the H-bond have been monitored using vibrational CyPy ring modes in FTIR spectra. The stabilization of the CyPy/TCA complex in its protonated form upon increasing polarity of the solvent has been evidenced. It was shown that formation of the CyPy/(TCA)(2) aggregates in the solutions favors the proton transfer process. An X-ray diffraction study has been performed on a single 1 : 2 co-crystal of pyridine/3,5-dinitrobenzoic acid. The H-bond motif found in this system exhibits the same connectivity by strong hydrogen bonds N-H(+)[dot dot dot]O(-) and O-H[dot dot dot]O as that in the CyPy/(TCA)(2) complex predicted by DFT calculation. Certain discrepancies are observed in C-H[dot dot dot]O connectivity only. The networks of H-bonds in both assemblies differ from those usually pictured for 1 : 2 base/carboxylic acid complexes in the literature.     

Characterization of the cation and temperature dependence of DNA quadruplex hydrogen bond properties using high-resolution NMR

Variations in the hydrogen bond network of the Oxy-1.5 DNA guanine quadruplex have been monitored by trans-H-bond scalar couplings, (h2)J(N2N7), for Na(+)-, K(+)-, and NH(4)(+)-bound forms over a temperature range from 5 to 55 degrees C. The variations in (h2)J(N2N7) couplings exhibit an overall trend of Na(+) > K(+) > NH(4)(+) and correlate with the different cation positions and N2-H2...N7 H-bond lengths in the respective structures. A global weakening of the (h2)J(N2N7) couplings with increasing temperature for the three DNA quadruplex species is accompanied by a global increase of the acceptor (15)N7 chemical shifts. Above 35 degrees C, spectral heterogeneity indicates thermal denaturation for the Na(+)-bound form, whereas spectral homogeneity persists up to 55 degrees C for the K(+)- and NH(4)(+)-coordinated forms. The average relative change of the (h2)J(N2N7) couplings amounts to approximately 0.8 x 10(-3)/K and is thus considerably smaller than respective values reported for nucleic acid duplexes. The significantly higher thermal stability of H-bond geometries in the DNA quadruplexes can be rationalized by their cation coordination of the G-quartets and the extensive H-bond network between the four strands. A detailed analysis of individual (h2)J(N2N7) couplings reveals that the 5' strand end, comprising base pairs G1-G9* and G4*-G1, is the most thermolabile region of the DNA quadruplex in all three cation-bound forms.     

Synthesis and X-ray diffraction analysis of coenzyme Q derivatives obtained from natural polyalkoxyallylbenzenes

A general synthetic access to methoxy analogues of coenzymes Q bearing functional substituents with various chain lengths at the quinone ring was developed using available natural (polymethoxy)(methylenedioxy)allylbenzenes. The Baeyer–Villiger rearrangement of (methylenedioxy)benzaldehydes into phenols followed by facile oxidation to quinones with the methylenedioxy moiety opening was identified as the key step in the synthesis of the target 1,4- and 1,2-polyalkoxyquinones