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1.
J Am Chem Soc ; 136(25): 9094-105, 2014 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-24884723

RESUMO

Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of two complexes [Mo(IV)O(bdt)2](2-) and [Mo(VI)O2(bdt)2](2-) (bdt = benzene-1,2-dithiolate(2-)) that relate to the reduced and oxidized forms of sulfite oxidase (SO). These are compared with those of previously studied dimethyl sulfoxide reductase (DMSOr) models. DFT calculations supported by the data are extended to evaluate the reaction coordinate for oxo transfer to a phosphite ester substrate. Three possible transition states are found with the one at lowest energy, stabilized by a P-S interaction, in good agreement with experimental kinetics data. Comparison of both oxo transfer reactions shows that in DMSOr, where the oxo is transferred from the substrate to the metal ion, the oxo transfer induces electron transfer, while in SO, where the oxo transfer is from the metal site to the substrate, the electron transfer initiates oxo transfer. This difference in reactivity is related to the difference in frontier molecular orbitals (FMO) of the metal-oxo and substrate-oxo bonds. Finally, these experimentally related calculations are extended to oxo transfer by sulfite oxidase. The presence of only one dithiolene at the enzyme active site selectively activates the equatorial oxo for transfer, and allows facile structural reorganization during turnover.


Assuntos
Proteínas com Ferro-Enxofre/metabolismo , Molibdênio/metabolismo , Oxirredutases/metabolismo , Teoria Quântica , Sulfito Oxidase/metabolismo , Enxofre/química , Tolueno/análogos & derivados , Proteínas com Ferro-Enxofre/química , Molibdênio/química , Oxirredutases/química , Oxigênio/química , Oxigênio/metabolismo , Sulfito Oxidase/química , Tolueno/química , Tolueno/metabolismo , Espectroscopia por Absorção de Raios X
2.
J Am Chem Soc ; 134(40): 16635-45, 2012 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-22974135

RESUMO

Photo-oxidations of hydrogen-bonded phenols using excited-state polyarenes are described to derive fundamental understanding of multiple-site concerted proton-electron transfer reactions (MS-CPET). Experiments have examined phenol bases having -CPh(2)NH(2), -Py, and -CH(2)Py groups ortho to the phenol hydroxyl group and tert-butyl groups in the 4,6-positions for stability (HOAr-NH(2), HOAr-Py, and HOAr-CH(2)Py, respectively; Py = pyridyl; Ph = phenyl). The photo-oxidations proceed by intramolecular proton transfer from the phenol to the pendent base concerted with electron transfer to the excited polyarene. For comparison, 2,4,6-(t)Bu(3)C(6)H(2)OH, a phenol without a pendent base and tert-butyl groups in the 2,4,6-positions, has also been examined. Many of these bimolecular reactions are fast, with rate constants near the diffusion limit. Combining the photochemical k(CPET) values with those from prior thermal stopped-flow kinetic studies gives data sets for the oxidations of HOAr-NH(2) and HOAr-CH(2)Py that span over 10(7) in k(CPET) and nearly 0.9 eV in driving force (ΔG(o)'). Plots of log(k(CPET)) vs ΔG(o)', including both excited-state anthracenes and ground state aminium radical cations, define a single Marcus parabola in each case. These two data sets are thus well described by semiclassical Marcus theory, providing a strong validation of the use of this theory for MS-CPET. The parabolas give λ(CPET) ≅ 1.15-1.2 eV and H(ab) ≅ 20-30 cm(-1). These experiments represent the most direct measurements of H(ab) for MS-CPET reactions to date. Although rate constants are available only up to the diffusion limit, the parabolas clearly peak well below the adiabatic limit of ca. 6 × 10(12) s(-1). Thus, this is a very clear demonstration that the reactions are nonadiabatic. The nonadiabatic character slows the reactions by a factor of ~45. Results for the oxidation of HOAr-Py, in which the phenol and base are conjugated, and for oxidation of 2,4,6-(t)Bu(3)C(6)H(2)OH, which lacks a base, show that both have substantially lower λ and larger pre-exponential terms. The implications of these results for MS-CPET reactions are discussed.


Assuntos
Fenóis/química , Transporte de Elétrons , Elétrons , Ligação de Hidrogênio , Oxirredução , Prótons , Termodinâmica
3.
Inorg Chem ; 51(6): 3436-42, 2012 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-22372518

RESUMO

Reaction coordinates for oxo transfer from the substrates Me(3)NO, Me(2)SO, and Me(3)PO to the biologically relevant Mo(IV) bis-dithiolene complex [Mo(OMe)(mdt)(2)](-) where mdt = 1,2-dimethyl-ethene-1,2-dithiolate(2-), and from Me(2)SO to the analogous W(IV) complex, have been calculated using density functional theory. In each case, the reaction first proceeds through a transition state (TS1) to an intermediate with substrate weakly bound, followed by a second transition state (TS2) around which breaking of the substrate X-O bond begins. By analyzing the energetic contributions to each barrier, it is shown that the nature of the substrate and metal determines which transition state controls the rate-determining step of the reaction.


Assuntos
Molibdênio/química , Compostos de Sulfidrila/química , Tungstênio/química , Espectroscopia por Absorção de Raios X
4.
J Phys Chem B ; 116(1): 571-84, 2012 Jan 12.
Artigo em Inglês | MEDLINE | ID: mdl-22148459

RESUMO

The oxidation of three phenols, which contain an intramolecular hydrogen bond to a pendent pyridine or amine group, has been shown, in a previous experimental study, to undergo concerted proton-electron transfer (CPET). In this reaction, the electron is transferred to an outer-sphere oxidant, and the proton is transferred from the oxygen to nitrogen atom. In the present study, this reaction is studied computationally using a version of Hammes-Schiffer's multistate continuum theory where CPET is formulated as a transmission frequency between neutral and cation vibrational-electronic states. The neutral and cation proton vibrational wave functions are computed from one-dimensional potential energy surfaces (PESs) for the transferring proton in a fixed heavy atom framework. The overlap integrals for these neutral/cation wave functions, considering several initial (i.e., neutral) and final (i.e., cation) vibrational states, are used to evaluate the relative rates of oxidation. The analysis is extended to heavy atom configurations with various proton donor-acceptor (i.e., O-N) distances to assess the importance of heavy atom "gating". Such changes in d(ON) dramatically affect the nature of the proton PESs and wave functions. Surprisingly, the most reactive configurations have similar donor-acceptor distances despite the large (~0.2 Å) differences in the optimized structures. These theoretical results qualitatively reproduce the experimental faster reactivity of the reaction of the pyridyl derivative 1 versus the CH(2)-pyridyl 2, but the computed factor of 5 is smaller than the experimental 10(2). The amine derivative is calculated to react similarly to 1, which does not agree with the experiments, likely due to some of the simplifying assumptions made in applying the theory. The computed kinetic isotope effects (KIEs) and their temperature dependence are in agreement with experimental results.


Assuntos
Elétrons , Fenol/química , Prótons , Ligação de Hidrogênio , Oxirredução , Teoria Quântica , Temperatura , Termodinâmica
5.
J Cheminform ; 3(1): 37, 2011 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-21999342

RESUMO

BACKGROUND: The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. RESULTS: This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. CONCLUSIONS: We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community.

6.
J Am Chem Soc ; 132(24): 8359-71, 2010 Jun 23.
Artigo em Inglês | MEDLINE | ID: mdl-20499905

RESUMO

Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of two Mo bis-dithiolene complexes, [Mo(OSi)(bdt)(2)](1-) and [MoO(OSi)(bdt)(2)](1-), where OSi = [OSiPh(2)(t)Bu](1-) and bdt = benzene-1,2-dithiolate(2-), that model the Mo(IV) and Mo(VI)=O states of the DMSO reductase family of molybdenum enzymes. These results show that the Mo(IV) complex undergoes metal-based oxidation unlike Mo tris-dithiolene complexes, indicating that the dithiolene ligands are behaving innocently. Experimentally validated calculations have been extended to model the oxo transfer reaction coordinate using dimethylsulfoxide (DMSO) as a substrate. The reaction proceeds through a transition state (TS1) to an intermediate with DMSO weakly bound, followed by a subsequent transition state (TS2) which is the largest barrier of the reaction. The factors that control the energies of these transition states, the nature of the oxo transfer process, and the role of the dithiolene ligand are discussed.


Assuntos
Proteínas com Ferro-Enxofre/química , Proteínas com Ferro-Enxofre/metabolismo , Molibdênio/química , Compostos Organometálicos/química , Oxirredutases/química , Oxirredutases/metabolismo , Teoria Quântica , Enxofre/química , Espectroscopia por Absorção de Raios X , Domínio Catalítico , Modelos Moleculares
8.
Inorg Chem ; 47(14): 6382-92, 2008 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-18517189

RESUMO

Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of a series of Mo tris(dithiolene) complexes, [Mo(mdt)3](z) (where mdt = 1,2-dimethylethene-1,2-dithiolate(2-) and z = 2-, 1-, 0), with near trigonal-prismatic geometries (D3h symmetry). These results show that the formally Mo(IV), Mo(V), and Mo(VI) complexes actually have a (dz(2))(2) configuration, that is, remain effectively Mo(IV) despite oxidation. Comparisons with the XAS data of another set of Mo tris(dithiolene) complexes, [Mo(tbbdt)3](z) (where tbbdt = 3,5-ditert-butylbenzene-1,2-dithiolate(2-) and z = 1-, 0), show that both neutral complexes, [Mo(mdt)3] and [Mo(tbbdt)3], have similar electronic structures while the monoanions do not. Calculations reveal that the "Bailar twist" present in the crystal structure of [Mo(tbbdt)3](1-) (D3 symmetry) but not [Mo(mdt)3](1-) (D3h symmetry) is controlled by electronic factors which arise from bonding differences between the mdt and tbbdt ligands. In the former, configuration interaction between the Mo d(z(2)) and a deeper energy, occupied ligand orbital, which occurs in D3 symmetry, destabilizes the Mo d(z(2)) to above another ligand orbital which is half-occupied in the D3h [Mo(mdt)3](1-) complex. This leads to a metal d(1) configuration with no ligand holes (i.e., d(1)[L3](0h)) for [Mo(tbbdt)3](1-) rather than the metal d(2) configuration with one ligand hole (i.e., d(2)[L3](1h)) for [Mo(mdt)3](1-). Thus, the Bailar twist observed in some metal tris(dithiolene) complexes is the result of configuration interaction between metal and ligand orbitals and can be probed experimentally by S K-edge XAS.


Assuntos
Molibdênio/química , Espectrofotometria Atômica , Enxofre/química , Modelos Moleculares , Estrutura Molecular
9.
J Comput Chem ; 29(5): 839-45, 2008 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-17849392

RESUMO

There are now a wide variety of packages for electronic structure calculations, each of which differs in the algorithms implemented and the output format. Many computational chemistry algorithms are only available to users of a particular package despite being generally applicable to the results of calculations by any package. Here we present cclib, a platform for the development of package-independent computational chemistry algorithms. Files from several versions of multiple electronic structure packages are automatically detected, parsed, and the extracted information converted to a standard internal representation. A number of population analysis algorithms have been implemented as a proof of principle. In addition, cclib is currently used as an input filter for two GUI applications that analyze output files: PyMOlyze and GaussSum.


Assuntos
Algoritmos , Simulação por Computador , Bases de Dados Factuais , Sistemas de Informação , Modelos Químicos , Software
10.
J Inorg Biochem ; 101(11-12): 1594-600, 2007 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-17720249

RESUMO

Molybdenum- or tungsten-containing enzymes catalyze oxygen atom transfer reactions involved in carbon, sulfur, or nitrogen metabolism. It has been observed that reduction potentials and oxygen atom transfer rates are different for W relative to Mo enzymes and the isostructural Mo/W complexes. Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations on [Mo(V)O(bdt)(2)](-) and [W(V)O(bdt)(2)](-), where bdt=benzene-1,2-dithiolate(2-), have been used to determine that the energies of the half-filled redox-active orbital, and thus the reduction potentials and MO bond strengths, are different for these complexes due to relativistic effects in the W sites.


Assuntos
Enzimas/química , Molibdênio/química , Compostos Organometálicos/química , Enxofre/química , Tungstênio/química , Absorciometria de Fóton , Enzimas/metabolismo , Estrutura Molecular , Oxirredução , Termodinâmica
11.
Biochemistry ; 42(48): 14214-24, 2003 Dec 09.
Artigo em Inglês | MEDLINE | ID: mdl-14640689

RESUMO

Zinc binding to the two Cys(4) sites present in the DNA-binding domain (DBD) of nuclear hormone receptor proteins is required for proper folding of the domain and for protein activity. By utilizing Co(2+) as a spectroscopic probe, we have characterized the metal-binding properties of the two Cys(4) structural zinc-binding sites found in the DBD of human estrogen receptor alpha (hERalpha-DBD) and rat glucocorticoid receptor (GR-DBD). The binding affinity of Co(2+) to the two proteins was determined relative to the binding affinity of Co(2+) to the zinc finger consensus peptide, CP-1. Using the known dissociation constant of Co(2+) from CP-1, the dissociation constants of cobalt from hERalpha-DBD were calculated: K(d1)(Co) = 2.2 (+/- 1.0) x 10(-7) M and K(d2)(Co) = 6.1 (+/- 1.5) x 10(-7) M. Similarly, the dissociation constants of Co(2+) from GR-DBD were calculated: K(d1)(Co) = 4.1 (+/- 0.6) x 10(-7) M and K(d2)(Co) = 1.7 (+/- 0.3) x 10(-7) M. Metal-binding studies conducted in which Zn(2+) displaces Co(2+) from the metal-binding sites of hERalpha-DBD and GR-DBD indicate that Zn(2+) binds to each of the Cys(4) metal-binding sites approximately 3 orders of magnitude more tightly than Co(2+) does: the stoichiometric dissociation constants are K(d1)(Zn) = 1 (+/- 1) x 10(-10) M and K(d2)(Zn) = 5 (+/- 1) x 10(-10) M for hERalpha-DBD and K(d1)(Zn) = 2 (+/- 1) x 10(-10) M and K(d2)(Zn) = 3 (+/- 1) x 10(-10) M for GR-DBD. These affinities are comparable to those observed for most other naturally occurring structural zinc-binding sites. In contrast to the recent prediction by Low et. al. that zinc binding in these systems should be cooperative [Low, L. Y., Hernández, H., Robinson, C. V., O'Brien, R., Grossmann, J. G., Ladbury, J. E., and Luisi, B. (2002) J. Mol. Biol. 319, 87-106], these data suggest that the zincs that bind to the two sites in the DBDs of hERalpha-DBD and GR-DBD do not interact.


Assuntos
Proteínas de Ligação a DNA/química , Fragmentos de Peptídeos/química , Receptores Estrogênicos/química , Receptores de Glucocorticoides/química , Zinco/química , Sequência de Aminoácidos , Animais , Ligação Competitiva/genética , Cobalto/química , Cobalto/metabolismo , Sequência Consenso/genética , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Receptor alfa de Estrogênio , Vetores Genéticos , Humanos , Ligantes , Modelos Moleculares , Dados de Sequência Molecular , Fragmentos de Peptídeos/genética , Fragmentos de Peptídeos/metabolismo , Ligação Proteica/genética , Estrutura Terciária de Proteína/genética , Ratos , Receptores Estrogênicos/genética , Receptores Estrogênicos/metabolismo , Receptores de Glucocorticoides/genética , Receptores de Glucocorticoides/metabolismo , Espectrofotometria Ultravioleta , Termodinâmica , Zinco/metabolismo , Dedos de Zinco/genética
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