PubMed Health⌕ Search

Biomedical subjects

Abhishek Dey

Publications and source records attributed to Abhishek Dey.

12 recordsLinked to original sources

A functional model for the cysteinate-ligated non-heme iron enzyme superoxide reductase (SOR).

Superoxide reductases (SORs) are cysteine-ligated, non-heme iron enzymes that reduce toxic superoxide radicals (O2-). The functional role of the trans cysteinate, as well as the mechanism by which SOR reduces O2-, is unknown. Herein is described a rare example of a functional metalloenzyme analogue, which catalytically reduces superoxide in a proton-dependent mechanism, via a trans thiolate-ligated iron-peroxo intermediate, the first example of its type. Acetic-acid-promoted H2O2 release, followed by Cp2Co reduction, regenerates the active Fe(II) catalyst. The thiolate ligand and its trans positioning relative to the substrate are shown to contribute significantly to the catalyst's function, by lowering the redox potential, changing the spin state, and dramatically lowering the nuFe-O stretching frequency well-below that of any other reported iron-peroxo, while leaving nuO-O high, so as to favor superoxide reduction and Fe-O, as opposed to O-O, bond cleavage. Thus we provide critical insight into the relationship between the SOR structure and its function, as well as important benchmark parameters for characterizing highly unstable thiolate-ligated iron-peroxo intermediates.

Catalysis↗

How does single oxygen atom addition affect the properties of an Fe-nitrile hydratase analogue? The compensatory role of the unmodified thiolate.

Nitrile hydratase (NHase) is one of a growing number of enzymes shown to contain post-translationally modified cysteine sulfenic acids (Cys-SOH). Cysteine sulfenic acids have been shown to play diverse roles in cellular processes, including transcriptional regulation, signal transduction, and the regulation of oxygen metabolism and oxidative stress responses. The function of the cysteine sulfenic acid coordinated to the iron active site of NHase is unknown. Herein we report the first example of a sulfenate-ligated iron complex, [Fe(III)(ADIT)(ADIT-O)](+) (5), and compare its electronic and magnetic properties with those of structurally related complexes in which the sulfur oxidation state and protonation state have been systematically altered. Oxygen atom addition was found to decrease the unmodified thiolate Fe-S bond length and blue-shift the ligand-to-metal charge-transfer band (without loss of intensity). S K-edge X-ray absorption spectroscopy and density functional theory calculations show that, although the modified RS-O(-) fragment is incapable of forming a pi bond with the Fe(III) center, the unmodified thiolate compensates for this loss of pi bonding by increasing its covalent bond strength. The redox potential shifts only slightly (75 mV), and the magnetic properties are not affected (the S = (1)/(2) spin state is maintained). The coordinated sulfenate S-O bond is activated and fairly polarized (S(+)-O(-)). Addition of strong acids at low temperatures results in the reversible protonation of sulfenate-ligated 5. An X-ray structure demonstrates that Zn(2+) binds to the sulfenate oxygen to afford [Fe(III)(ADIT)(ADIT-O-ZnCl(3))] (6). The coordination of ZnCl(3)(-) to the RS-O(-) unit causes the covalent overlap with the unmodified thiolate to increase further. A possible catalytic role for the unmodified NHase thiolate, involving its ability to "tune" the electronics in response to protonation of the sulfenate (RS-O(-)) oxygen and/or substrate binding, is discussed.

Hydro-Lyases↗

X-ray absorption spectroscopy and density functional theory studies of [(H3buea)FeIII-X]n- (X = S2-, O2-, OH-): comparison of bonding and hydrogen bonding in oxo and sulfido complexes.

Iron L-edge, iron K-edge, and sulfur K-edge X-ray absorption spectroscopy was performed on a series of compounds [Fe(III)H(3)buea(X)](n-) (X = S(2-), O(2-), OH(-)). The experimentally determined electronic structures were used to correlate to density functional theory calculations. Calculations supported by the data were then used to compare the metal-ligand bonding and to evaluate the effects of H-bonding in Fe(III)(-)O vs Fe(III)(-)S complexes. It was found that the Fe(III)(-)O bond, while less covalent, is stronger than the Fe(III)(-)S bond. This dominantly reflects the larger ionic contribution to the Fe(III)(-)O bond. The H-bonding energy (for three H-bonds) was estimated to be -25 kcal/mol for the oxo as compared to -12 kcal/mol for the sulfide ligand. This difference is attributed to the larger charge density on the oxo ligand resulting from the lower covalency of the Fe-O bond. These results were extended to consider an Fe(IV)(-)O complex with the same ligand environment. It was found that hydrogen bonding to Fe(IV)(-)O is less energetically favorable than that to Fe(III)(-)O, which reflects the highly covalent nature of the Fe(IV)(-)O bond.

Absorptiometry, Photon↗

Sulfur K-edge XAS and DFT calculations on nitrile hydratase: geometric and electronic structure of the non-heme iron active site.

The geometric and electronic structure of the active site of the non-heme iron enzyme nitrile hydratase (NHase) is studied using sulfur K-edge XAS and DFT calculations. Using thiolate (RS(-))-, sulfenate (RSO(-))-, and sulfinate (RSO(2)(-))-ligated model complexes to provide benchmark spectral parameters, the results show that the S K-edge XAS is sensitive to the oxidation state of S-containing ligands and that the spectrum of the RSO(-) species changes upon protonation as the S-O bond is elongated (by approximately 0.1 A). These signature features are used to identify the three cysteine residues coordinated to the low-spin Fe(III) in the active site of NHase as CysS(-), CysSOH, and CysSO(2)(-) both in the NO-bound inactive form and in the photolyzed active form. These results are correlated to geometry-optimized DFT calculations. The pre-edge region of the X-ray absorption spectrum is sensitive to the Z(eff) of the Fe and reveals that the Fe in [FeNO](6) NHase species has a Z(eff) very similar to that of its photolyzed Fe(III) counterpart. DFT calculations reveal that this results from the strong pi back-bonding into the pi antibonding orbital of NO, which shifts significant charge from the formally t(2)(6) low-spin metal to the coordinated NO.

Binding Sites↗

Metal-thiolate bonds in bioinorganic chemistry.

Metal-thiolate active sites play major roles in bioinorganic chemistry. The M--S(thiolate) bonds can be very covalent, and involve different orbital interactions. Spectroscopic features of these active sites (intense, low-energy charge transfer transitions) reflect the high covalency of the M--S(thiolate) bonds. The energy of the metal-thiolate bond is fairly insensitive to its ionic/covalent and pi/sigma nature as increasing M--S covalency reduces the charge distribution, hence the ionic term, and these contributions can compensate. Thus, trends observed in stability constants (i.e., the Irving-Williams series) mostly reflect the dominantly ionic contribution to bonding of the innocent ligand being replaced by the thiolate. Due to high effective nuclear charges of the Cu(II) and Fe(III) ions, the cupric- and ferric-thiolate bonds are very covalent, with the former having strong pi and the latter having more sigma character. For the blue copper site, the high pi covalency couples the metal ion into the protein for rapid directional long range electron transfer. For rubredoxins, because the redox active molecular orbital is pi in nature, electron transfer tends to be more localized in the vicinity of the active site. Although the energy of hydrogen bonding of the protein environment to the thiolate ligands tends to be fairly small, H-bonding can significantly affect the covalency of the metal-thiolate bond and contribute to redox tuning by the protein environment.

Chemistry, Bioinorganic↗

Sulfur K-edge XAS and DFT calculations on [Fe4S4]2+ clusters: effects of H-bonding and structural distortion on covalency and spin topology.

Sulfur K-edge X-ray absorption spectroscopy of a hydrogen-bonded elongated [Fe4S4]2+ cube is reported. The data show that this synthetic cube is less covalent than a normal compressed cube with no hydrogen bonding. DFT calculations reveal that the observed difference in electronic structure has significant contributions from both the cluster distortion and from hydrogen bonding. The elongated and compressed Fe4S4 structures are found to have different spin topologies (i.e., orientation of the delocalized Fe2S2 subclusters which are antiferromagnetically coupled to each other). It is suggested that the H-bonding interaction with the counterion does not contribute to the cluster elongation. A magneto-structural correlation is developed for the Fe4S4 cube that is used to identify the redox-active Fe2S2 subclusters in active sites of HiPIP and ferredoxin proteins involving these clusters.

Bacterial Proteins↗

Sulfur K-edge XAS and DFT calculations on P450 model complexes: effects of hydrogen bonding on electronic structure and redox potentials.

Hydrogen bonding (H-bonding) is generally thought to play an important role in tuning the electronic structure and reactivity of metal-sulfur sites in proteins. To develop a quantitative understanding of this effect, S K-edge X-ray absorption spectroscopy (XAS) has been employed to directly probe ligand-metal bond covalency, where it has been found that protein active sites are significantly less covalent than their related model complexes. Sulfur K-edge XAS data are reported here on a series of P450 model complexes with increasing H-bonding to the ligated thiolate from its substituent. The XAS spectroscopic results show a dramatic decrease in preedge intensity. DFT calculations reproduce these effects and show that the observed changes are in fact solely due to H-bonding and not from the inductive effect of the substituent on the thiolate. These calculations also indicate that the H-bonding interaction in these systems is mainly dipolar in nature. The -2.5 kcal/mol energy of the H-bonding interaction was small relative to the large change in ligand-metal bond covalency (30%) observed in the data. A bond decomposition analysis of the total energy is developed to correlate the preedge intensity change to the change in Fe-S bonding interaction on H-bonding. This effect is greater for the reduced than the oxidized state, leading to a 260 mV increase in the redox potential. A simple model shows that E degrees should vary approximately linearly with the covalency of the Fe-S bond in the oxidized state, which can be determined directly from S K-edge XAS.

Binding Sites↗

Ligand K-edge X-ray absorption spectroscopy and DFT calculations on [Fe3S4]0,+ clusters: delocalization, redox, and effect of the protein environment.

Ligand K-edge XAS of an [Fe3S4]0 model complex is reported. The pre-edge can be resolved into contributions from the mu(2)S(sulfide), mu(3)S(sulfide), and S(thiolate) ligands. The average ligand-metal bond covalencies obtained from these pre-edges are further distributed between Fe(3+) and Fe(2.5+) components using DFT calculations. The bridging ligand covalency in the [Fe2S2]+ subsite of the [Fe3S4]0 cluster is found to be significantly lower than its value in a reduced [Fe2S2] cluster (38% vs 61%, respectively). This lowered bridging ligand covalency reduces the superexchange coupling parameter J relative to its value in a reduced [Fe2S2]+ site (-146 cm(-1) vs -360 cm(-1), respectively). This decrease in J, along with estimates of the double exchange parameter B and vibronic coupling parameter lambda2/k(-), leads to an S = 2 delocalized ground state in the [Fe3S4]0 cluster. The S K-edge XAS of the protein ferredoxin II (Fd II) from the D. gigas active site shows a decrease in covalency compared to the model complex, in the same oxidation state, which correlates with the number of H-bonding interactions to specific sulfur ligands present in the active site. The changes in ligand-metal bond covalencies upon redox compared with DFT calculations indicate that the redox reaction involves a two-electron change (one-electron ionization plus a spin change of a second electron) with significant electronic relaxation. The presence of the redox inactive Fe(3+) center is found to decrease the barrier of the redox process in the [Fe3S4] cluster due to its strong antiferromagnetic coupling with the redox active Fe2S2 subsite.

Binding Sites↗

Ligand K-edge X-ray absorption spectroscopy of [Fe4S4]1+,2+,3+ clusters: changes in bonding and electronic relaxation upon redox.

Sulfur K-edge X-ray absorption spectroscopy (XAS) is reported for [Fe(4)S(4)](1+,2+,3+) clusters. The results are quantitatively and qualitatively compared with DFT calculations. The change in covalency upon redox in both the [Fe(4)S(4)](1+/2+) (ferredoxin) and the [Fe(4)S(4)](2+/3+) (HiPIP) couple are much larger than that expected from just the change in number of 3d holes. Moreover, the change in the HiPIP couple is higher than that of the ferredoxin couple. These changes in electronic structure are analyzed using DFT calculations in terms of contributions from the nature of the redox active molecular orbital (RAMO) and electronic relaxation. The results indicate that the RAMO of HiPIP has 50% ligand character, and hence, the HiPIP redox couple involves limited electronic relaxation. Alternatively, the RAMO of the ferredoxin couple is metal-based, and the ferredoxin redox couple involves extensive electronic relaxation. The contributions of these RAMO differences to ET processes in the different proteins are discussed.

Electron Transport↗

Beta-octafluorocorroles.

The one-pot corrole synthesis first reported by the Gross and Paolesse groups appears to have evolved into a remarkably general and predictable self-assembly based synthetic reaction. Gross's solvent-free procedure (refs 8 and 9) has proven particularly effective in our hands and, in fact, more general than originally claimed. In earlier work (ref 17), we showed that the reaction works for a variety of aromatic aldehyde starting materials and was not limited to relatively electron-deficient aldehydes, as reported by Gross and co-workers. Here, we show that the pyrrole component is also variable in that 3,4-difluoropyrrole undergoes oxidative condensation with four different p-X-substituted benzaldehydes to yield the corresponding beta-octafluoro-meso-tris(para-X-phenyl)corroles (X = CF3, H, CH3, and OCH3). Further, we have prepared the Cu and FeCl derivatives of the beta-octafluorocorrole ligands. The XPS nitrogen 1s ionization potentials of these fluorinated ligands are some 0.7 eV higher than those of the corresponding beta-unfluorinated ligands. The oxidation half-wave potentials of the Cu and FeCl complexes of the fluorinated corroles are also positively shifted by 300-400 mV relative to their beta-unsubstituted analogues, demonstrating the strongly electron-deficient character of the fluorinated ligands. 1H NMR spectroscopy suggests that like their beta-unfluorinated counterparts, the new beta-octafluorinated triarylcorroles act as substantially noninnocent ligands, i.e., exhibit corrole pi-cation radical character, in the FeCl complexes. Quantitatively, however, NMR spectroscopy and DFT calculations indicate that the beta-octafluorinated corroles are somewhat less noninnocent (i.e., carry less radical character) than their beta-unfluorinated counterparts in the FeCl complexes. Temperature-dependent 19F NMR spectroscopy suggests that the Cu octafluorocorroles have a thermally accessible paramagnetic excited state, which we assign as a Cu(II) corrole pi-cation radical. We have previously reported that the electronic absorption spectra, particularly the Soret absorption maxima, of high-valent transition metal triarylcorroles are very sensitive to the nature of the substituents in the meso positions. In contrast, the Soret absorption maxima of free-base triarylcorroles are not particularly sensitive to the nature of the meso substituents. This scenario also holds for the fluorinated corroles described here. Thus, although the four free-base fluorinated triarylcorroles exhibit practically identical Soret absorption maxima, the Soret bands of the Cu derivatives of the same corroles red-shift by approximately 35 nm on going from the p-CF3 to the p-OCH3 derivative.

Journal Article↗

30pi aromatic meso-substituted heptaphyrin isomers: syntheses, characterization, and spectroscopic studies.

The syntheses of new aromatic 30pi heptaphyrins either through a [5 + 2] or a [4 + 3] acid-catalyzed condensation and oxidative coupling reactions of easily available and air-stable precursors are reported. The methodology followed is not only simple and efficient but also allows synthesis of a range of heptaphyrins with different heteroatoms in the core. The oxidative coupling reactions of modified tripyrranes 11 and tetrapyrranes 12 were found to be dependent on the acid concentration used and as well as the substituents present on the meso position. The change of meso aryl substituents in 11 and 12 to meso mesityl substituents gave a new heptaphyrin 18. The structural characterization has been done with extensive 1H and 2D NMR studies. The heptaphyrins reported here show rich structural diversity when the connections of the heterocyclic rings are altered, and accordingly, one ring and two ring inversions have been observed. By a judicious choice of the precursors it has been possible to control the site of ring inversion either in the bithiophene unit or in the tripyrrane unit. Theoretical calculations performed on three different heptaphyrins, 4, 5, and 17, also reveal that the inverted structures are approximately 35-40 kJ lower in energy relative to the corresponding noninverted structures. Furthermore, one of the heptaphyrins 10c shows the presence of two conformers in solution in the ratio 1:2 and no interconversion between the conformers have been observed in the temperature range of 343-228 K. On protonation, the aromaticity and the ring inversions are retained and the deltadelta values vary in the range 10.07-20.59 ppm. The energies of the Soret maxima and the HOMO-LUMO gap vary linearly with the increase in pi electrons further justifying the aromatic nature of the heptaphyrins.

Journal Article↗

"True" iron(V) and iron(VI) porphyrins: a first theoretical exploration.

We present here a first theoretical characterization of iron(V) (S = (3)/(2)) and iron(VI) (S = 0) porphyrin intermediates. The Fe(V) calculations exhibit exceptionally narrow convergence radii and we believe that for this reason they have long eluded researchers working on high-valent iron intermediates. The Fe(V)-N(nitrido) bond distance in the DFT(PW91/TZP) optimized geometry of Fe(V)(P)(N) is 1.722 A, comparable to and slightly longer than the Fe(IV)-O bond distance of 1.684 A in Fe(IV)(P)(O) and the Fe(IV)-N(imido) bond distance of 1.698 A in Fe(IV)(P)(NH). In contrast, the Fe(VI)-N(nitrido) bond distances in [Fe(VI)(P)(N)](+) (S = 0) and Fe(VI)(P)(N)(F) (S = 0) are dramatically shorter, 1.508 and 1.533 A, respectively, consistent with the formal triple bond character of the Fe(VI)-N(nitrido) bond. The nitrido ligand appears to be uniquely capable of stabilizing a "true" Fe(V) center, in the sense defined in the paper. All three unpaired electrons in Fe(V)(P)(N) are completely localized on the Fe(V)-N(nitrido) axis, with the Fe and N gross atomic spin populations being 1.579 and 1.550, respectively. In contrast, an axial ligand set consisting of an oxide and a fluoride do not stabilize an Fe(V) ground state but favor an electronic structure best described as an Fe(IV)-oxo porphyrin pi-cation radical.

Heme↗