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ABSTRACT: The competitive adsorption of Nafion functional groups induce complex potential dependencies (Stark tuning) of vibrational modes of CO adsorbed (CO(ads)) on the Pt of operating fuel cell electrodes. Operando infrared (IR) spectroscopy, polarization modulated IR spectroscopy (PM-IRRAS) of Pt-Nafion interfaces, and attenuated total reflectance IR spectroscopy of bulk Nafion were correlated by density functional theory (DFT) calculated spectra to elucidate Nafion functional group coadsorption responsible for the Stark tuning of CO(ads) on high surface area fuel cell electrodes. The DFT calculations and observed spectra suggest that the side-chain CF(3), CF(2) groups (i.e., of the backbone and side chain) and the SO(3)(-) are ordered by the platinum surface. A model of the Nafion-Pt interface with appropriate dihedral and native bond angles, consistent with experimental and calculated spectra, suggest direct adsorption of the CF(3) and SO(3)(-) functional groups on Pt. Such adsorption partially orders the Nafion backbone and/or side-chain CF(2) groups relative to the Pt surface. The coadsorption of CF(3) is further supported by Mulliken partial charge calculations: The CF(3) fluorine atoms have the highest average charge among all types of Nafion fluorine atoms and are second only to the sulfonate oxygen atoms.
Journal of the American Chemical Society 11/2010; · 9.91 Impact Factor
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06/2010;
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ABSTRACT: Density functional theory (DFT) and x-ray absorption fine structure (XAFS) spectroscopy are complementary tools for the biophysical study of active sites in metalloproteins. DFT is used to compute XAFS multiple scattering Debye Waller factors, which are then employed in genetic algorithm-based fitting process to obtain a global fit to the XAFS in the space of fitting parameters. Zn-Cys sites, which serve important functions as transcriptional switches in Zn finger proteins and matrix metalloproteinases, previously have proven intractable by this method; here these limitations are removed. In this work we evaluate optimal DFT nonlocal functionals and basis sets for determining optimal geometries and vibrational densities of states of mixed ligation Zn(His)(4-n)(Cys)(n) sites. Theoretical results are compared to experimental XAFS measurements and Raman spectra from the literature and tabulated for use.
The Journal of Chemical Physics 04/2008; 128(11):115104. · 3.33 Impact Factor
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ABSTRACT: X-ray absorption fine structure is a powerful tool for probing the structures of metals in proteins in both crystalline and noncrystalline environments. Until recently, a fundamental problem in biological XAFS has been that ad hoc assumptions must be made concerning the vibrational properties of the amino acid residues that are coordinated to the metal to fit the data. Here, an automatic procedure for accurate structural determination of active sites of metalloproteins is presented. It is based on direct multiple-scattering simulation of experimental X-ray absorption fine structure spectra combining electron multiple scattering calculations with density functional theory calculations of vibrational modes of amino acid residues and the genetic algorithm differential evolution to determine a global minimum in the space of fitting parameters. Structure determination of the metalloprotein active site is obtained through a self-consistent iterative procedure with only minimal initial information.
Biophysical Journal 01/2007; 91(11):L87-9. · 3.65 Impact Factor
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ABSTRACT: The C-O stretching frequency (nu(CO)) of atop CO/Pt in PtRu alloys is compositionally tuned in proportion to the Pt mole percent. The application of a Blyholder-Bagus type mechanism (i.e., increased back-donation from the metal d-band to the hybridized 2pi CO molecular orbitals (MOs)) to compositional tuning has been paradoxical because (1) a Pt-C bond contraction, expected with increased back-donation as the Pt mole percent is reduced, is not observed (i.e., calculated Pt-C bond is either elongated or insensitive to alloying and the binding energies of CO/Pt decrease with alloying) and (2) the lowering d-band center and increased d-band vacancies upon alloying (suggesting less back-donation to the higher energy metal hybridized 2pi CO MOs) must be reconciled with the alloy-induced red shift of the nu(CO). A library of spin-optimized Pt and Pt alloy clusters was the basis of density functional theory (DFT) calculations of CO binding energies, nu(CO) values, shifts, and broadening of 5sigma/2pi CO MO upon hybridization with the alloy orbitals and a DFT derived Mulliken electron population analysis. The DFT results, combined with FEFF8 local density of states (LDOS) calculations, validate a 5sigma donation-2pi back-donation mechanism, reconciling the direction of alloy compositional tuning with the lowering of the d-band center and increased vacancies. Although the d-band center decreases in energy with alloying, an asymmetric increase in the dispersion of the d-band is accompanied by an upshift of the metal cluster HOMO level. Concomitantly, the hybridization and renormalization of the CO 5sigma/2pi states results in a broadening of the 5sigma/2pi manifold with additional lower energy states closer to the upshifted (with respect to the pure Pt cluster) HOMO of the alloy cluster. The dispersion toward higher energies of the alloy d-density of states results in more 5sigma/2pi CO filled states (i.e., enhanced 2pi-back-donation). Finally, Mulliken and FEFF8 electron population analysis shows that the increase of the average d-band vacancies upon alloying and additional 2pi back-donation are not mutually exclusive. The d-electron density of the CO-adsorbed Pt atom increases with alloying while the average d-electron density throughout the cluster is reduced. The localized electron density is manifested as an electrostatic wall effect, preventing the Pt-C bond contractions expected with increased back-donation to the 2pi CO MOs.
The Journal of Physical Chemistry B 03/2005; 109(5):1839-48. · 3.70 Impact Factor
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ABSTRACT: Data analysis is one of the remaining bottlenecks in high-throughput EXAFS for structural genomics. Here some recent developments in methodology are described that offer the potential for rapid and automated XAS analysis of metalloproteins.
Journal of Synchrotron Radiation 02/2005; 12(Pt 1):53-6. · 2.73 Impact Factor
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ABSTRACT: The extended x-ray-absorption fine structure (EXAFS) Debye-Waller factor is an essential term appearing in the EXAFS equation that accounts for the molecular structural and thermal disorder of a sample. Single- and multiple-scattering Debye-Waller factors must be known accurately to obtain quantitative agreement between theory and experiment. Since the total number of fitting parameters that can be varied is limited in general, data cannot support fitting of all relevant multiple-scattering Debye-Waller factors. Calculation of the Debye-Waller factors is typically done using the correlated Debye approximation, where a single parameter (Debye temperature) is varied. However, this procedure cannot account in general for Debye-Waller factors in materials with heterogeneous bond strengths, such as biomolecules. As an alternative procedure in this work, we calculate them ab initio directly from the known or hypothetical three-dimensional structure. In this paper we investigate the adequacy of various computational approaches for calculating vibrational structure within small molecules. Detailed EXAFS results will be presented in a subsequent paper. Analytical expressions are derived for multiple scattering Debye-Waller factors, based on the plane wave approximation. Semiempirical Hamiltonians and the ab initio density functional method are used to calculate the normal mode eigenfrequencies and eigenvectors. These data are used to calculate all single- and multiple-scattering Debye-Waller factors up to a four atom cluster. These ab initio Debye-Waller factors are compared to those calculated from experimental infrared and Raman frequencies. As an example comparison with experimental EXAFS data from GeCl4, GeH3Cl gases are also reported. Good agreement is observed for all cases tested.
Phys. Rev. B. 07/1998; 58(5).
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ABSTRACT: X-ray absorption fine structure (XAFS) spectroscopy is one of the few direct probes of the structure of metalloprotein binding that is equally applicable to proteins in crystals, solutions, and membranes. Despite considerable progress in the calculation of the photoelectron scattering aspects of XAFS, calculation of the vibrational aspects has lagged because of the difficulty of the calculations. We report here initial results that express single- and multiple-scattering Debye-Waller factors as polynomial functions of first shell radial distance for metal-peptide complexes, enabling quantitatively accurate full multiple-scattering XAFS data analysis of active sites of unknown structure at arbitrary temperatures without the use of ad hoc assumptions.
Phys. Rev. B. 65(20).
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ABSTRACT: An accurate and practical method for the calculation and use of thermal x-ray absorption fine structure (XAFS) Debye-Waller factors (DWFs) in active sites of metalloproteins is presented. These factors are calculated on model clusters within the local density functional approximation with nonlocal corrections. The DWFs are mapped out and parametrized as a function of the first shell distance and an angle (where applicable), for all significant single and multiple scattering paths, as well as the sample temperature. This approach is applied to the biologically essential but spectroscopically silent Zn+2 active sites composed of histidines, cysteines, and carboxylate ligands in homogeneous and heterogeneous environments. Detailed analysis of the relative scattering paths for Zn metalloproteins using projected vibrational density of states further explain why these paths are not detectable by XAFS for first shell metal-ligand distances above a “cutoff” value.
Phys. Rev. B. 70(19).
