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At least 289 records · Page 16Linked to original sources

The electronic structure of liquid water within density-functional theory.

In the last decade, computational studies of liquid water have mostly concentrated on ground-state properties. However, recent spectroscopic measurements have been used to infer the structure of water, and the interpretation of optical and x-ray spectra requires accurate theoretical models of excited electronic states, not only of the ground state. To this end, we investigate the electronic properties of water at ambient conditions using ab initio density-functional theory within the generalized gradient approximation (DFT/GGA), focusing on the unoccupied subspace of Kohn-Sham eigenstates. We generate long (250 ps) classical trajectories for large supercells, up to 256 molecules, from which uncorrelated configurations of water molecules are extracted for use in DFT/GGA calculations of the electronic structure. We find that the density of occupied states of this molecular liquid is well described with 32-molecule supercells using a single k point (k=0) to approximate integration over the first Brillouin zone. However, the description of the unoccupied electronic density of states (u-EDOS) is sensitive to finite size effects. Small, 32-molecule supercell calculations, using the Gamma-point approximation, yield a spuriously isolated state above the Fermi level. Nevertheless, the more accurate u-EDOS of large, 256-molecule supercells may be reproduced using smaller supercells and increased k-point sampling. This indicates that the electronic structure of molecular liquids such as water is relatively insensitive to the long-range disorder in the molecular structure. These results have important implications for efficiently increasing the accuracy of spectral calculations for water and other molecular liquids.

Journal Article↗

A new kind of fasciolicide: molecular and electronic structures of some o-hydroxybenzenesulfonanilides.

The molecular and electronic structures of some fasciolicidal o-hydroxybenzenesulfonanilides (HBSA) have been studied using X-ray diffraction and semiempirical MO calculation. In these compounds, the phenolic hydroxyl forms a strong intramolecular hydrogen bond with an adjacent sulfonyl oxygen atom and the strength of the d-p dative S<--N bond, which may control the electron delocalization throughout the entire molecule, is affected by substituents on the phenyl rings on both sides. Owing to the poor delocalization, the contribution of the keto-form of the resonance structure is larger for some phenolate anions of HBSA in solution, and this may be a key factor determining the potency of fasciolicidal activity of HBSA.

Anilides↗

On the "Rebound" Mechanism of Alkane Hydroxylation by Cytochrome P450: Electronic Structure of the Intermediate and the Electron Transfer Character in the Rebound Step.

Two electromeric forms, a and b (a is the ground state in a solvent) exist for the hydroxo-iron complex 1, an intermediate in the rebound mechanism of alkane hydroxylation by cytochrome P450. Results of density functional and model solvent calculations of various species are in agreement with experimental findings, and imply the role of 1 a in the rebound mechanism.

Journal Article↗

The electronic structure of nonpolyhex carbon nanotubes.

Generalizing the folding method to any periodic two-dimensional planar carbon structures we have calculated the corresponding electronic structures in the framework of the one orbital one site tight-binding (Bloch-Hückel) method by solving the eigenvalue problems in a numerical way. We discussed the metallic or the nonmetallic behavior of the nanotubes by applying the folding vectors of parameters (m, n). We extended the topological coordinate method to two-dimensional periodic planar structures as well. Nearly regular hexagonal, pentagonal, and heptagonal polygons were obtained. The curvatures of the final relaxed structures can be read from the sizes of the polygons. Thus relying only on the topological information we could describe the shape of the tubular structures and their conductivity behaviors.

Journal Article↗

[Electron structure of plastoquinone and coupling of electron and proton transport in thylakoids of the higher plants].

The energy dependence on hydrogen position for a system, consisting of plastoquinone (in different redox states) and histidine molecules was studied. The distance between the atoms forming the hydrogen bond, an oxygen of the quinone molecule and a nitrogen of histidine, was supposed to be fixed. It was shown that for neutral quinone the total energy is minimal when the hydrogen is bound to histidine; for reduced quinone, the probability of hydrogen binding to quinone and histidine is approximately equal (so that a hydrogen bond is formed) and on secondary reduction of plastoquinone, the hydrogen binds to it.

Electron Transport↗

Electronic structures of acyl nitrites and nitrates.

The gas phase electronic structures of CM(3)C(O)ONO and CM(3)C(O)ONO(2) (M=H, Cl, F) are studied by photoelectron spectroscopy (PES) combined with the outer valence Green's function (OVGF) calculations at 6-311+G(d, p) basis sets. The highest occupied molecular orbital (HOMO) for each compound is the carbonyl oxygen lone pair (n(O)), the ionizations of these orbitals are associated with the vibrational frequency about 1750 and 1820 cm(-1) reflected on the first band, respectively, for acyl nitrites and nitrate. Comparing with the calculated energies, it can be concluded that the syn conformers with Cs overall symmetry, a planar CC(O)ONO skeleton in nitrites, and a planar CC(O)ON skeleton in nitrates, respectively, are the most stable in the gas phase.

Electrons↗

Spectroscopic and computational study of a non-heme iron [Fe-NO]7 system: exploring the geometric and electronic structures of the nitrosyl adduct of iron superoxide dismutase.

Like many non-heme iron enzymes, reduced iron superoxide dismutase (Fe(2+)SOD) reacts with nitric oxide (NO) to yield an [Fe-NO]7 system. Electron paramagnetic resonance (EPR) data obtained for this Fe-NO adduct of FeSOD (NO-FeSOD) exhibit two rhombic S = 3/2 signals of comparable population; E/D = 0.128 (42%) and 0.154 (58%). While similar results were previously reported for NO-FeSOD [Niederhoffer, E. C.; Fee, J. A.; Papaefthymiou, V.; Münck, E. Magnetic Resonance Studies Involving Iron Superoxide Dismutase from Escherichia coli. Isotope and Nuclear Chemistry Division Annual Report; Los Alamos National Laboratory: Los Alamos, NM, 1987], detailed geometric and electronic structure descriptions of these [Fe-NO]7 systems had not yet been developed. Therefore, in addition to EPR spectroscopy, we have used electronic absorption, magnetic circular dichroism (MCD), variable-temperature, variable-field MCD, and resonance Raman spectroscopies to determine ground-state spin Hamiltonian parameters, electronic transition energies, oscillator strengths, and transition polarizations for NO-FeSOD. These spectroscopic parameters have been used in conjunction with density functional theory (DFT) and semiempirical INDO/S-CI calculations to generate an experimentally calibrated active site model for NO-FeSOD. Our studies indicate that NO binds to the active site of Fe(2+)SOD to form a six-coordinate [Fe-NO]7 system with an Fe-N-O angle of approximately 145 degrees. DFT computations performed on this model of NO-FeSOD reveal that the NO ligand is formally reduced by the ferrous center to yield NO(-) and an Fe(3+) center that are strongly antiferromagnetically coupled. DFT calculations reveal that NO binding to Fe(2+)SOD also lowers the pK of the coordinated water ligand by at least 3.3 pH units, suggesting that this process is associated with increased acidity and probable ionization of the axial solvent ligand. To explore the origin of the two [Fe-NO]7 systems observed by EPR spectroscopy, additional calculations have been performed on slightly perturbed NO-FeSOD models. Significantly, semiempirical INDO/S-CI computations reveal that the rhombicity of NO-FeSOD is altered by changes in the Fe-N-O angle or rotation about the Fe-N(O) bond, suggesting that the two species observed by EPR spectroscopy merely differ slightly with respect to the orientation of the NO ligand. Indeed, our EPR data obtained on NO-FeSOD variants indicate that the relative population of the S = 3/2 signals can be altered by perturbations in the second sphere of the protein active site. These results provide compelling evidence that the second coordination sphere is able to modulate the geometric and electronic structures of NO-FeSOD.

Binding Sites↗

Electronic structure of the surface of the ionic liquid [EMIM][Tf(2)N] studied by metastable impact electron spectroscopy (MIES), UPS, and XPS.

The near-surface electronic structure of the room-temperature ionic liquid (RT-IL) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM][Tf(2)N]) has been investigated with the combination of the electron spectroscopies metastable impact electron spectroscopy (MIES), ultraviolet photoelectron spectroscopy (UPS (HeI and HeII)), and monochromatized X-ray photoelectron spectroscopy (XPS). We find that the top of the valence band states originates from states of the cation (see also ref 1). The ultimately surface-sensitive technique MIES proves that the surface layer consists of both cations and anions. The temperature dependence of the spectra has been measured between about 160 and 610 K. Information on the glass transition and the possibility for low-temperature distillation of [EMIM][Tf(2)N] at reduced pressures is derived from the present results.

Journal Article↗

Critical appraisal of electronic structure of metmyoglobin. 14N and 57Fe hyperfine interactions.

The electronic structure of metmyoglobin is subjected to a critical examination by comparison of results of recent ENDOR measurements of nitrogen hyperfine interaction constants on the porphyrin ring and on the proximal histidine linking the heme to the protein with theoretical values for these properties from calculated electronic wavefunctions for this molecule. The observed interesting trends of the 14N hyperfine data as well as available 57Fe data are both successfully explained showing that theory has provided a satisfactory description of the electronic distribution in this important molecule.

Ferric Compounds↗

Electronic structure of DNA by DV-X alpha cluster calculations: II. d(GG).d(CC), d(CG)2, d(GC)2 A and B conformations. (Part 2) Sugars and bases.

The electronic structure of d(GG).d(CC), d(CG)2, d(GC)2 which are stacked base pairs in the DNA double helix, are elucidated for both A and B conformations in detail by DV-X alpha cluster calculations. These three DNA double helix fragments are contracted from the same bases, G and C, but the electronic structures of the fragments for both A and B conformations are different from each other characteristically. There are some delicate differences in the admixture of the orbital components and the overlap populations of intra- and inter- strand stacked bases among the stacking isomers. On the other hand, the electronic states of sugars differ in the 5'-3' direction, but are not almost dependent on stacked base pairs.

Cytosine Nucleotides↗

Comparative quantum-chemical analysis of the electronic structure and Mössbauer parameters of the active site models for deoxymyoglobin and alpha- and beta-subunits of tetrameric deoxyhemoglobin.

The results of iterative extended Huckel calculations of the electronic structure of the penta-coordinated Fe(II)-porphyn-imidazole complexes as models for deoxymyoglobin and alpha- and beta-subunits of tetrameric deoxyhemoglobin are presented. Temperature dependences of the Fe-57 nuclei quadrupole splitting and isomer shift for deoxymyoglobin and alpha- and beta-subunits of tetrameric deoxyhemoglobin models were calculated taking into account the spin-orbit coupling between ground and low-lying Fe(II) high spin terms. The results show that the electronic structure and Mössbauer parameters are sensitive to the stereochemical differences of the active sites in deoxymyoglobin and alpha- and beta-subunits of tetrameric deoxyhemoglobin.

Binding Sites↗

Local electronic structure of layered Li(x)Ni0.5Mn0.5O2 and Li(x)Ni(1/3)Mn(1/3)Co(1/3)O2.

Samples of Li(x)Ni0.5Mn0.5O2 and Li(x)Ni(1/3)Mn(1/3)Co(1/3)O2 were prepared as active materials in electrochemical half-cells and were cycled electrochemically to obtain different values of Li concentration, x. Absorption edges of Ni, Mn, Co, and O in these materials of differing x were measured by electron energy loss spectrometry (EELS) in a transmission electron microscope to determine the changes in local electronic structure caused by delithiation. The work was supported by electronic structure calculations with the VASP pseudopotential package, the full-potential linear augmented plane wave code WIEN2K, and atomic multiplet calculations that took account of the electronic effects from local octahedral symmetry. A valence change from Ni2+ to Ni4+ with delithiation would have caused a 3 eV shift in energy of the intense white line at the Ni L3 edge, but the measured shift was less than 1.2 eV. The intensities of the "white lines" at the Ni L-edges did not change enough to account for a substantial change of Ni valence. No changes were detectable at the Mn and Co L-edges after delithiation either. Both EELS and the computational efforts showed that most of the charge compensation for Li+ takes place at hybridized O 2p states, not at Ni atoms.

Journal Article↗

Effect of surface composition on electronic structure, stability, and electrocatalytic properties of Pt-transition metal alloys: Pt-skin versus Pt-skeleton surfaces.

The surface properties of PtM (M = Co, Ni, Fe) polycrystalline alloys are studied by utilizing Auger electron spectroscopy, low energy ion scattering spectroscopy, and ultraviolet photoemission spectroscopy. For each alloy initial surface characterization was done in an ultrahigh vacuum (UHV) system, and depending on preparation procedure it was possible to form surfaces with two different compositions. Due to surface segregation thermodynamics, annealed alloy surfaces form the outermost Pt-skin surface layer, which consists only platinum atoms, while the sputtered surfaces have the bulk ratio of alloying components. The measured valence band density of state spectra clearly shows the differences in electronic structures between Pt-skin and sputtered surfaces. Well-defined surfaces were hereafter transferred out from UHV and exposed to the acidic (electro)chemical environment. The electrochemical and post-electrochemical UHV surface characterizations revealed that Pt-skin surfaces are stable during and after immersion to an electrolyte. In contrast all sputtered surfaces formed Pt-skeleton outermost layers due to dissolution of transition metal atoms. Therefore, these three different near-surface compositions (Pt-skin, Pt-skeleton, and pure polycrystalline Pt) all having pure-Pt outermost layers are found to have different electronic structures, which originates from different arrangements of subsurface atoms of the alloying component. Modification in Pt electronic properties alters adsorption/catalytic properties of the corresponding bimetallic alloy. The most active systems for the electrochemical oxygen reduction reaction are established to be the Pt-skin near-surface composition, which also have the most shifted metallic d-band center position versus Fermi level.

Journal Article↗