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1.
J Comput Chem ; 44(32): 2486-2500, 2023 Dec 15.
Artículo en Inglés | MEDLINE | ID: mdl-37650712

RESUMEN

The recent discovery that anaerobic methanogens can reductively dissolve pyrite and utilize dissolution products as a source of iron and sulfur to meet their biosynthetic demands for these elements prompted the development of atomic-scale nanoparticle models, as maquettes of reactive surface sites, for describing the fundamental redox steps that take place at the mineral surface during reduction. The given report describes our computational approach for modeling n(FeS2 ) nanoparticles originated from mineral bulk structure. These maquettes contain a comprehensive set of coordinatively unsaturated Fe(II) sites that are connected via a range of persulfide (S2 2- ) ligation. In addition to the specific maquettes with n = 8, 18, and 32 FeS2 units, we established guidelines for obtaining low-energy structures by considering the pattern of ionic, covalent, and magnetic interactions among the metal and ligand sites. The developed models serve as computational nano-reactors that can be used to describe the reductive dissolution mechanism of pyrite to better understand the reactive sites on the mineral, where microbial extracellular electron-transfer reactions can occur.

2.
Org Biomol Chem ; 21(29): 5953-5963, 2023 07 26.
Artículo en Inglés | MEDLINE | ID: mdl-37199112

RESUMEN

Peptide bond formation is a fundamental organic chemical reaction; however, despite numerous recent reports, the computationally predicted barriers remain contradictory to experimental results. Incompleteness of the molecular mechanism for either the peptide bond formation or the reverse hydrolysis reactions is also highlighted by our lack of understanding of the seemingly equilibrium nature of the reaction that favors dipeptide formation over longer peptide chains under hydrothermal conditions. In this work, we first completed an assessment of levels of theory and evaluated chemical models that range from the neutral glycine condensation reaction in gas phase to explicitly solvated zwitterionic amino acids that are embedded in a polarizable continuum at neutral pH. Ultimately, we identified a six-step 'ping-pong' mechanism with the involvement of both zwitterions and neutral species. The carboxylate and amine end-groups of the diglycine intermediates play critical roles in the proton transfer and condensation processes. The experimental condensation barrier of 98 kJ mol-1 was approximated to be 118-129 kJ mol-1 at the MN15/def2TZVPP|SMD(water) level of theory for the rate determining step, when using the most complete model for the solvation environment. Condensed phase free energy correction employed to the rate limiting step reduced the barrier height to 106 kJ mol-1. These results have fundamental implications for understanding enzyme catalyzed peptide bond formation, peptide/protein stability, and "metabolism first" emergence of life scenarios.


Asunto(s)
Péptidos , Protones , Modelos Moleculares , Hidrólisis , Termodinámica , Péptidos/química , Agua/química
3.
Angew Chem Int Ed Engl ; 62(1): e202213462, 2023 Jan 02.
Artículo en Inglés | MEDLINE | ID: mdl-36279321

RESUMEN

We report a nickel complex for catalytic oxidation of ammonia to dinitrogen under ambient conditions. Using the aryloxyl radical 2,4,6-tri-tert-butylphenoxyl (t Bu3 ArO⋅) as a H atom acceptor to cleave the N-H bond of a coordinated NH3 ligand up to 56 equiv of N2 per Ni center can be generated. Employing the N-oxyl radical 2,2,6,6-(tetramethylpiperidin-1-yl)oxyl (TEMPO⋅) as the H-atom acceptor, up to 15 equiv of N2 per Ni center are formed. A bridging Ni-hydrazine product identified by isotopic nitrogen (15 N) studies and supported by computational models indicates the N-N bond forming step occurs by bimetallic homocoupling of two paramagnetic [Ni]-NH2 fragments. Ni-mediated hydrazine disproportionation to N2 and NH3 completes the catalytic cycle.

4.
Phys Chem Chem Phys ; 24(46): 28121-28126, 2022 Nov 30.
Artículo en Inglés | MEDLINE | ID: mdl-36412497

RESUMEN

Incorporation of heteroatoms in carbon materials is commonly expected to influence their physical or chemical properties. However, contrary to previous results for methane adsorption, no technologically significant effect was identified for the hydrogen physisorption energies (measured 4.1-4.6 kJ mol-1 and calculated qst = -ΔHads = 4.1 ± 0.7 kJ mol-1 using a comprehensive set of levels of theory) as a function of B- and N-substitution of a mid-plane C-site on open carbon surfaces.

5.
J Synchrotron Radiat ; 28(Pt 6): 1825-1838, 2021 Nov 01.
Artículo en Inglés | MEDLINE | ID: mdl-34738936

RESUMEN

Sulfur K-edge X-ray absorption spectroscopy (XAS) was employed to experimentally characterize the coordinative bond between the thiourea (TU) or thiocarbamide ligand and transition metal (TM) ions Zn2+, Co2+ and Ni2+ in distorted tetrahedral and octahedral homoleptic coordination environments. Comparisons of XAS spectra of the free TU ligand and [Zn(TU)4]2+, [Co(TU)4]2+ and [Ni(TU)6]2+ complexes clearly identify spectral features unique to TM2+-S(TU) bonding. Quantitative analysis of pre-edge intensities describes the covalency of Ni2+-S(TU) and Co2+-S(TU) bonding to be at most 21% and 9% as expressed by the S 3p contributions per TM 3d electron hole. Using relevant Ni2+ complexes with dithiocarbamate and thioether ligands, we evaluated the empirical S 1s → 3p transition dipole integrals developed for S-donor ligands and their dependence on heteroatom substitutions. With the aid of density functional theory-based ground electronic state calculations, we found evidence for the need of using a transition dipole that is dependent on the presence of conjugated heteroatom (N) substitution in these S-donor ligands.


Asunto(s)
Compuestos Organometálicos , Tiourea , Electrónica , Azufre , Espectroscopía de Absorción de Rayos X , Zinc
6.
J Phys Chem A ; 125(28): 6042-6058, 2021 Jul 22.
Artículo en Inglés | MEDLINE | ID: mdl-34232640

RESUMEN

Experimental and theoretical studies disagree on the energetics of methane adsorption on carbon materials. However, this information is critical for the rational design and optimization of the structure and composition of adsorbents for natural gas storage. The delicate nature of dispersion interactions, polarization of both the adsorbent and the adsorbate, interplay between H-bonding and tetrel bonding, and induced dipole/Coulomb interactions inherent to methane physisorption require computational treatment at the highest possible level of theory. In this study, we employed the smallest reasonable computational model, a maquette of porous carbon surfaces with a central site for substitution and methane binding. The most accurate predictions of methane adsorption energetics were achieved by electron-correlated molecular orbital theory CCSD(T) and hybrid density functional theory MN15 calculations employing a saturated, all-electron basis set. The characteristic geometry of methane adsorption on a carbon surface ("lander approach") arises due to bonding interactions of the adsorbent π-system with the proximal H-C bonds of methane, in addition to tetrel bonding between the antibonding orbital of the distal C-H bond and the central atom of the maquette (C, B, or N). The polarization of the electron density, structural deformations, and the comprehensive energetic analysis clearly indicate a ∼3 kJ mol-1 preference for methane binding on the N-substituted maquette. The B-substituted maquette showed a comparable or lower binding energy than the unsubstituted, pure C model, depending on the level of theory employed. The calculated thermodynamic results indicate a strategy for incorporating electron-enriched substitutions (e.g., N) into carbon materials as a way to increase methane storage capacity over electron-deficient (e.g., B) modifications. The thermochemical analysis was revised for establishing a conceptual agreement between the experimental isosteric heat of adsorption and the binding enthalpies from statistical thermodynamics principles.

7.
J Org Chem ; 85(2): 1315-1321, 2020 01 17.
Artículo en Inglés | MEDLINE | ID: mdl-31830417

RESUMEN

The role of the chemical environment in promoting anthralin/O2 reactions was discovered using neat solvents to model the amino acids of a cofactor-independent oxygenase. Experimental and computational results highlight the importance of the substrate-enolate, which is accessed via energetically small, escalating steps in which the ground-state keto-isomer is tautomerized to an enol and then ionized by solvent. The resulting ion-pair is poised for spontaneous electron transfer to O2. Similar activation may be exploited in biological/nonbiological oxidations involving O2.

8.
J Comput Chem ; 40(2): 515-526, 2019 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-30548652

RESUMEN

Peptides coordinated to iron-sulfur clusters, referred to as maquettes, represent a synthetic strategy for constructing biomimetic models of iron-sulfur metalloproteins. These maquettes have been successfully employed as building blocks of engineered heme-containing proteins with electron-transfer functionality; however, they have yet to be explored in reactivity studies. The concept of iron-sulfur nesting in peptides is a leading hypothesis in Origins-of-Life research as a plausible path to bridge the discontinuity between prebiotic chemical transformations and extant enzyme catalysis. Based on past biomimetic and biochemical research, we put forward a mechanism of maquette reconstitution that guides our development of computational tools and methodologies. In this study, we examined a key feature of the first stage of maquette formation, which is the secondary structure of aqueous peptide models using molecular dynamics simulations based on the AMBER99SB empirical force field. We compared and contrasted S…S distances, [2Fe-2S] and [4Fe-4S] nests, and peptide conformations via Ramachandran plots for dissolved Cys and Gly amino acids, the CGGCGGC 7-mer, and the GGCGGGCGGCGGW 16-mer peptide. Analytical tools were developed for following the evolution of secondary structural features related to [Fe-S] cluster nesting along 100 ns trajectories. Simulations demonstrated the omnipresence of peptide nests for preformed [2Fe-2S] clusters; however, [4Fe-4S] cluster nests were observed only for the 16-mer peptide with lifetimes of a few nanoseconds. The origin of the [4Fe-4S] nest and its stability was linked to a "kinked-ribbon" peptide conformation. Our computational approach lays the foundation for transitioning into subsequent stages of maquette reconstitution, those being the formation of iron ion/iron-sulfur coordinated peptides. © 2018 Wiley Periodicals, Inc.


Asunto(s)
Proteínas Hierro-Azufre/química , Simulación de Dinámica Molecular , Péptidos/química , Aminoácidos/química , Hidrólisis , Estructura Secundaria de Proteína
9.
J Biol Inorg Chem ; 24(6): 793-807, 2019 09.
Artículo en Inglés | MEDLINE | ID: mdl-31486952

RESUMEN

The synthesis and characterization of short peptide-based maquettes of metalloprotein active sites facilitate an inquiry into their structure/function relationships and evolution. The [4Fe-4S]-maquettes of bacterial ferredoxin metalloproteins (Fd) have been used in the past to engineer redox active centers into artificial metalloenzymes. The novelty of our study is the application of maquettes to the superfamily of [4Fe-4S] cluster and S-adenosylmethionine-dependent radical metalloenzymes (radical SAM). The radical SAM superfamily enzymes contain site-differentiated, redox active [4Fe-4S] clusters coordinated to Cx3Cx2C or related motifs, which is in contrast to the Cx2Cx2C motif found in bacterial ferredoxins (Fd). Under an optimized set of experimental conditions, a high degree of reconstitution (80-100%) was achieved for both radical SAM- and Fd-maquettes. Negligible chemical speciation was observed for all sequences, with predominantly [4Fe-4S]2+ for the 'as-reconstituted' state. However, the reduction of [4Fe-4S]2+-maquettes provides low conversion (7-17%) to the paramagnetic [4Fe-4S]+ state, independent of either the spacing of the cysteine residues (Cx3Cx2C vs. Cx2Cx2C), the nature of intervening amino acids, or the length of the cluster binding motif. In the absence of the stabilizing protein environment, the reduction process is proposed to proceed via [4Fe-4S]2+ cluster disassembly and reassembly in a more reduced state. UV-Vis and EPR spectroscopic techniques are employed as analytical tools to quantitate the as-reconstituted (or oxidized) and one-electron reduced states of the [4Fe-4S] clusters, respectively. We demonstrate that short Fd and radical SAM derived 7- to 9-mer peptides containing appropriate cysteine motifs function equally well in coordinating redox active [4Fe-4S] clusters.


Asunto(s)
Péptido C/química , S-Adenosilmetionina/química , Cisteína/química , Ferredoxinas/química , Proteínas Hierro-Azufre/química
10.
J Phys Chem A ; 123(1): 343-358, 2019 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-30540469

RESUMEN

In order to define a robust level of theory using density functionals for investigating the reactivity of ruthenium complexes, we used benchmark wave function theory, with saturated basis sets to validate generalized gradient approximation (GGA), meta-GGA, and hyper-GGA functionals in the presence and absence of empirical dispersion and range-separated corrections. We first selected potentially suitable functionals that gave accurate predictions of the relative energetics of coordination isomers. These functionals were further evaluated for the chemical accuracy of their predicted geometric and electronic structures. For the latter, both the ionic and covalent interactions were considered. The reference level of theory for comparison was coupled-cluster perturbation theory using full treatment of singles and doubles (CCSD) with a saturated triple-ζ quality basis set (TZVP) and corresponding small-core, effective core potentials for ruthenium. Several population analysis methods were evaluated to predict the ionic interactions. We found that the atomic charges obtained from fitting the electrostatic potential provided the most reasonable estimates for the ruthenium complexes. The covalent interactions were quantified by considering the atomic compositions of Ru 4d x2- y2- and 4d z2-based frontier unoccupied orbitals. Comparison of more than two dozen functionals with reference data from high-level wave function calculations revealed trends that allowed for the formulation of an optimal hybrid density functional: PBE exchange and correlation functionals with 50% HF exchange component. This level of theory was found to reproduce the experimental structure of Ru(II) complexes. These complexes were used to investigate chemical speciation in a simplified model for an ionic liquid environment.

11.
Inorg Chem ; 57(12): 7151-7167, 2018 Jun 18.
Artículo en Inglés | MEDLINE | ID: mdl-29874059

RESUMEN

A procedure is developed for defining a compositionally and structurally realistic, atomic-scale description of exfoliated clay nanoparticles from the kaolinite family of phylloaluminosilicates. By use of coordination chemical principles, chemical environments within a nanoparticle can be separated into inner, outer, and peripheral spheres. The edges of the molecular models of nanoparticles were protonated in a validated manner to achieve charge neutrality. Structural optimizations using semiempirical methods (NDDO Hamiltonians and DFTB formalism) and ab initio density functionals with a saturated basis set revealed previously overlooked molecular origins of morphological changes as a result of exfoliation. While the use of semiempirical methods is desirable for the treatment of nanoparticles composed of tens of thousands of atoms, the structural accuracy is rather modest in comparison to DFT methods. We report a comparative survey of our infrared data for untreated crystalline and various exfoliated states of kaolinite and halloysite. Given the limited availability of experimental techniques for providing direct structural information about nano-kaolinite, the vibrational spectra can be considered as an essential tool for validating structural models. The comparison of experimental and calculated stretching and bending frequencies further justified the use of the preferred level of theory. Overall, an optimal molecular model of the defect-free, ideal nano-kaolinite can be composed with respect to stationary structure and curvature of the potential energy surface using the PW91/SVP level of theory with empirical dispersion correction (PW91+D) and polarizable continuum solvation model (PCM) without the need for a scaled quantum chemical force field. This validated theoretical approach is essential in order to follow the formation of exfoliated clays and their surface reactivity that is experimentally unattainable.

12.
Langmuir ; 33(14): 3534-3547, 2017 04 11.
Artículo en Inglés | MEDLINE | ID: mdl-28290695

RESUMEN

Surface modifications fundamentally influence the morphology of kaolinite nanostructures as a function of crystallinity and the presence of contaminants. Besides morphology, the catalytic properties of 1:1-type exfoliated aluminosilicates are also influenced by the presence of defect sites that can be generated in a controlled manner by mechanochemical activation. In this work, we investigated exfoliated halloysite nanoparticles with a quasi-homogeneous, scroll-type secondary structure toward developing structural/functional relationships for composition, atomic structure, and morphology. The surface properties of thin-walled nanoscrolls were studied as a function of mechanochemical activation expressed by the duration of dry-grinding. The surface characterizations were carried out using N2, NH3, and CO2 adsorption measurements. The effects of grinding on the nanohalloysite structure were followed using thermoanalytical thermogravimetric/derivative thermogravimetric (TG/DTG) and infrared spectroscopic [Fourier transform infrared/attenuated total reflection (FTIR/ATR)] techniques. Grinding results in partial dehydroxylation with similar changes as those observed for heat treatment above 300 °C. Mechanochemical activation shows a decrease in the dehydroxylation mass loss and the DTG peak temperature, a decrease in the specific surface area and the number of mesopores, an increase in the surface acidity, blue shift of surface hydroxide bands, and a decrease in the intensity of FTIR/ATR bands as a function of the grinding time. The experimental observations were used to guide atomic-scale structural and energetic simulations using realistic molecular cluster models for a nanohalloysite particle. A full potential energy surface description was developed for the mechanochemical activation and/or heating toward nanometahalloysite formation that aids the interpretation of experimental results. The calculated differences upon dehydroxylation show a remarkable agreement with the mass loss values from DTG measurements.

13.
Inorg Chem ; 56(3): 1080-1093, 2017 Feb 06.
Artículo en Inglés | MEDLINE | ID: mdl-28068071

RESUMEN

Sulfur K-edge X-ray absorption spectroscopy (XAS) spectra of the monodentate sulfate complexes [MII(itao)(SO4)(H2O)0,1] (M = Co, Ni, Cu) and [Cu(Me6tren)(SO4)] exhibit well-defined preedge transitions at 2479.4, 2479.9, 2478.4, and 2477.7 eV, respectively, despite having no direct metal-sulfur bond, while the XAS preedge of [Zn(itao)(SO4)] is featureless. The sulfur K-edge XAS of [Cu(itao)(SO4)] but not of [Cu(Me6tren)(SO4)] 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 [MII(SO4)(H2O)] (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 (α) and spin-down (ß) 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 0.5-2 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 copper(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 metal-absorber bond. The 2472.1 eV transition is evidence for further radicalization from copper(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.


Asunto(s)
Compuestos Organometálicos/química , Sulfatos/química , Azufre/química , Elementos de Transición/química , Transporte de Electrón , Ligandos , Teoría Cuántica , Espectroscopía de Absorción de Rayos X
14.
J Comput Chem ; 37(18): 1681-96, 2016 07 05.
Artículo en Inglés | MEDLINE | ID: mdl-27117497

RESUMEN

The structural properties and reactivity of iron-sulfur proteins are greatly affected by interactions between the prosthetic groups and the surrounding amino acid residues. Thus, quantum chemical investigations of the structure and properties of protein-bound iron-sulfur clusters can be severely limited by truncation of computational models. The aim of this study was to identify, a priori, significant interactions that must be included in a quantum chemical model. Using the [2Fe-2S] accessory cluster of the FeFe-hydrogenase as a demonstrative example with rich electronic structural features, the electrostatic and covalent effects of the surrounding side chains, charged groups, and backbone moieties were systematically mapped through density functional theoretical calculations. Electron affinities, spin density differences, and delocalization indexes from the quantum theory of atoms in molecules were used to evaluate the importance of each interaction. Case studies for hydrogen bonding and charged side-chain interactions were used to develop selection rules regarding the significance of a given protein environmental effect. A set of general rules is proposed for constructing quantum chemical models for iron-sulfur active sites that capture all significant interactions from the protein environment. This methodology was applied to our previously used models in galactose oxidase and the 6Fe-cluster of FeFe-hydrogenase. © 2016 Wiley Periodicals, Inc.


Asunto(s)
Simulación por Computador , Ambiente , Proteínas Hierro-Azufre/química , Hierro/química , Modelos Químicos , Azufre/química , Enlace de Hidrógeno , Modelos Moleculares , Teoría Cuántica
15.
J Biol Inorg Chem ; 21(5-6): 757-75, 2016 09.
Artículo en Inglés | MEDLINE | ID: mdl-27350153

RESUMEN

The linear nickel-nitrosyl complex [Ni(NO)(L3)] supported by a highly hindered tridentate nitrogen-based ligand, hydrotris(3-tertiary butyl-5-isopropyl-1-pyrazolyl)borate (denoted as L3), was prepared by the reaction of the potassium salt of the ligand with the nickel-nitrosyl precursor [Ni(NO)(Br)(PPh 3 ) 2 ]. The obtained nitrosyl complexes as well as the corresponding chlorido complexes [Ni(NO)(Cl)(PPh 3 ) 2 ] and [Ni(Cl)(L3)] were characterized by X-ray crystallography and different spectroscopic methods including IR/far-IR, UV-Vis, NMR, and multi-edge X-ray absorption spectroscopy at the Ni K-, Ni L-, Cl K-, and P K-edges. For comparative electronic structure analysis we also performed DFT calculations to further elucidate the electronic structure of [Ni(NO)(L3)]. These results provide the nickel oxidation state and the character of the Ni-NO bond. The complex [Ni(NO)(L3)] is best described as [Ni (II) (NO (-) )(L3)], and the spectroscopic results indicate that the phosphane complexes have a similar [Ni (II) (NO (-) )(X)(PPh 3 ) 2 ] ground state.


Asunto(s)
Níquel/química , Óxidos de Nitrógeno/química , Compuestos Organometálicos/química , Cristalografía por Rayos X , Electrones , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Estructura Molecular , Compuestos Organometálicos/síntesis química , Teoría Cuántica , Espectrofotometría Infrarroja , Espectrofotometría Ultravioleta , Espectroscopía de Absorción de Rayos X
16.
J Phys Chem A ; 119(22): 5579-86, 2015 Jun 04.
Artículo en Inglés | MEDLINE | ID: mdl-25923832

RESUMEN

X-ray absorption spectroscopy is a unique experimental technique that can provide ground state electronic structure information about transition metal complexes with unoccupied d-manifold. The quantitative treatments of pre-edge and rising-edge features have already been developed for the sulfur- and chlorine-ligand K-edge excitations. The complementarity of using multiple core excitation edges from hard, tender, and soft X-ray energy regions has been defined for the first paper of this series. The given study provides compelling evidence for the transferability of the empirical transition dipole integral from ligand K-edge to metal L-edge and back to ligand K-edge in the tender X-ray energy range. The case study was performed for a series of homoleptic chloropalladium compounds at the chlorine K- and palladium L-edges. We propose the method described here to be generally applicable for other core level excitations, where complementarity of ground state electronic structural information from XANES analysis can provide the complete electronic structure description.

17.
J Comput Chem ; 35(7): 540-52, 2014 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-24458434

RESUMEN

The covalent character of iron-sulfur bonds is a fundamental electronic structural feature for understanding the electronic and magnetic properties and the reactivity of biological and biomimetic iron-sulfur clusters. Conceptually, bond covalency obtained from X-ray absorption spectroscopy (XAS) can be directly related to orbital compositions from electronic structure calculations, providing a standard for evaluation of density functional theoretical methods. Typically, a combination of functional and basis set that optimally reproduces experimental bond covalency is chosen, but its dependence on the population analysis method is often neglected, despite its important role in deriving theoretical bond covalency. In this study of iron tetrathiolates, and classical [2Fe-2S] and [4Fe-4S] clusters with only thiolate ligands, we find that orbital compositions can vary significantly depending on whether they are derived from frontier orbitals, spin densities, or electron sharing indexes from "Átoms in Molecules" (ÁIM) theory. The benefits and limitations of Mulliken, Minimum Basis Set Mulliken, Natural, Coefficients-Squared, Hirshfeld, and AIM population analyses are described using ab initio wave function-based (QCISD) and experimental (S K-edge XAS) bond covalency. We find that the AIM theory coupled with a triple-ζ basis set and the hybrid functional B(5%HF)P86 gives the most reasonable electronic structure for the studied Fe-S clusters.


Asunto(s)
Proteínas Hierro-Azufre/química , Hierro/química , Compuestos de Sulfhidrilo/química , Azufre/química , Electrones , Ligandos , Modelos Moleculares , Espectroscopía de Absorción de Rayos X
18.
J Biol Inorg Chem ; 19(3): 465-83, 2014 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-24532333

RESUMEN

Spore photoproduct lyase (SPL), a member of the radical S-adenosyl-L-methionine (SAM) superfamily, catalyzes the direct reversal of the spore photoproduct, a thymine dimer specific to bacterial spores, to two thymines. SPL requires SAM and a redox-active [4Fe-4S] cluster for catalysis. Mössbauer analysis of anaerobically purified SPL indicates the presence of a mixture of cluster states with the majority (40 %) as [2Fe-2S](2+) clusters and a smaller amount (15 %) as [4Fe-4S](2+) clusters. On reduction, the cluster content changes to primarily (60 %) [4Fe-4S](+). The speciation information from Mössbauer data allowed us to deconvolute iron and sulfur K-edge X-ray absorption spectra to uncover electronic (X-ray absorption near-edge structure, XANES) and geometric (extended X-ray absorption fine structure, EXAFS) structural features of the Fe-S clusters, and their interactions with SAM. The iron K-edge EXAFS data provide evidence for elongation of a [2Fe-2S] rhomb of the [4Fe-4S] cluster on binding SAM on the basis of an Fe···Fe scatterer at 3.0 Å. The XANES spectra of reduced SPL in the absence and presence of SAM overlay one another, indicating that SAM is not undergoing reductive cleavage. The X-ray absorption spectroscopy data for SPL samples and data for model complexes from the literature allowed the deconvolution of contributions from [2Fe-2S] and [4Fe-4S] clusters to the sulfur K-edge XANES spectra. The analysis of pre-edge features revealed electronic changes in the Fe-S clusters as a function of the presence of SAM. The spectroscopic findings were further corroborated by density functional theory calculations that provided insights into structural and electronic perturbations that can be correlated by considering the role of SAM as a catalyst or substrate.


Asunto(s)
Hierro/análisis , Proteínas/fisiología , S-Adenosilmetionina/análisis , Espectroscopía de Absorción de Rayos X/métodos , Hierro/química , Hierro/metabolismo , Unión Proteica/fisiología , S-Adenosilmetionina/química , S-Adenosilmetionina/metabolismo , Espectroscopía de Mossbauer/métodos , Esporas Bacterianas/enzimología , Esporas Bacterianas/fisiología
19.
Inorg Chem ; 53(16): 8191-3, 2014 Aug 18.
Artículo en Inglés | MEDLINE | ID: mdl-25102222

RESUMEN

The α-ketocarboxylatocopper(II) complex [{Cu(L1)}{O2CC(O)CH(CH3)2}] can be spontaneously converted into the binuclear oxalatocopper(II) complex [{Cu(L1)}2(µ-C2O4)] upon exposure to O2/CO2 gas. (13)C-labeling experiments revealed that oxalate ions partially incorporated (13)CO2 molecules. Furthermore, the bicarbonatocopper(I) complex (NEt4)[Cu(L1){O2C(OH)}] in an Ar atmosphere and the α-ketocarboxylatocopper(I) complex Na[Cu(L1){O2CC(O)CH(CH3)2}] in an O2 atmosphere were also transformed spontaneously into the oxalato complex [{Cu(L1)}2(µ-C2O4)].

20.
Inorg Chem ; 53(19): 10195-202, 2014 Oct 06.
Artículo en Inglés | MEDLINE | ID: mdl-25254603

RESUMEN

One-electron-oxidized Ni(III)-phenoxide complexes with salen-type ligands, [Ni(salen)py2](2+) ([1(en)-py](2+)) and [Ni(1,2-salcn)py2](2+) ([1(cn)-py](2+)), with a five-membered chelate dinitrogen backbone and [Ni(salpn)py2](2+) ([2(pn)-py](2+)), with a six-membered chelate backbone, have been characterized with a combination of experimental and theoretical methods. The five-membered chelate complexes [1(en)-py](2+) and [1(cn)-py](2+) were assigned as Ni(III)-phenoxyl radical species, while the six-membered chelate complex [2(pn)-py](2+) was concluded to be a Ni(II)-bis(phenoxyl radical) species with metal-centered reduction in the course of the one-electron oxidation of the Ni(III)-phenoxide complex [2(pn)-py](+). Thus, the oxidation state of the one-electron-oxidized Ni(III) salen-type complexes depends on the chelate ring size of the dinitrogen backbone.


Asunto(s)
Níquel/química , Compuestos Organometálicos/química , Óxidos/química , Electrones , Ligandos , Estructura Molecular , Compuestos Organometálicos/síntesis química , Oxidación-Reducción
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