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PubMed2005

Electronic structure of Ag2Cu2O4. Evidence of oxidized silver and copper and internal charge delocalization.

The electronic structure of the recently isolated silver copper oxide Ag(2)Cu(2)O(4) is analyzed along with its precursor Ag(2)Cu(2)O(3) and similar binary oxides, Ag(2)O, AgO, CuO, and NaCuO(2), using X-ray photoemission (XPS) and X-ray absorption (XAS) measurements. The results for Ag(2)Cu(2)O(4) reveal an electronic distribution in which silver and copper share a delocalized valence scheme with both metals in formal oxidation states larger than the usual Ag(I) and Cu(II). Only one type of crystallographic silver or copper is found, but disorder-strain parameters are considerable and the possibilities of thermal disorder, atomic motion, oxygen contribution, mixed valence, and internal charge delocalization are considered. Classical coordination descriptions for oxidized silver are revisited in terms of this new internal charge delocalization framework found for the electronic structure.

Copper↗
PubMed1999

Chemical Transport Synthesis, Electrochemical Behavior, and Electronic Structure of Superconducting Zirconium and Hafnium Nitride Halides.

The layered nitrides beta-MNX (M = Zr, Hf; X = Cl, Br) crystallize in the space group R&thremacr;m with a hexagonal cell of dimensions a = 3.6031(6) Å, c = 27.672(2) Å for beta-ZrNCl, a = 3.5744(3) Å, c = 27.7075(9) Å for beta-HfNCl, and a = 3.6379(5) Å, c = 29.263(2) Å for beta-ZrNBr. Lithium intercalation using n-buthyllithium in hexane solutions leads to solvent free superconductors of formula Li(0.20)ZrNCl, Li(0.42)HfNCl, Li(0.67)HfNCl, and Li(0.17)ZrNBr showing critical temperatures of 12, 18, 24, and 13.5 K, respectively. Whereas several samples of beta-ZrNBr and beta-ZrNCl showed reproducibility in the lithium uptake and in the corresponding critical temperatures, different samples of beta-HfNCl subjected to the same treatment in n-buthyllithium showed lithium uptakes ranging from 0.07 to 0.67, and corresponding critical temperatures between 0 and 24 K. A linear dependence of T(c) versus the lithium content is observed when all the superconducting samples are considered. The results obtained from electrochemical lithiation are consistent with those obtained with chemical methods, as samples with larger capacity on discharge are also those found to have larger lithium contents after chemical lithiation. Most samples present a reduction step around 1.8 V vs Li(0)-Li(+) whose origin is still unclear. The electrochemical capacity on discharge for beta-HfNCl and beta-ZrNBr depends on the milling time spent in the preparation of the electrodes, with long milling times resulting in lower intercalation degree. Possible causes for this effect are either the creation of structural defects (e.g., stacking faults) or some sample decomposition induced by local heating. The same phenomena are proposed to account for the different behavior of beta-HfNCl samples, although additional aspects such as the presence of hydrogen, oxygen, or extra hafnium atoms in the structure have to be considered. Tight-binding band structure calculations for beta-MNX (M = Zr, X = Cl, Br; M = Hf, X = Cl), ZrCl, and Y(2)C(2)Br(2) are reported. The density of states and Fermi surfaces of the beta-MNX phases as well as the relationship between the electronic structure of the beta-ZrNCl and ZrCl are discussed. Despite the structural relationships, the electronic structures near the Fermi level of the beta-MNX and Y(2)Br(2)C(2) phases are found to be very different.

Journal Article↗
PubMed2006

Electronic structure and charge transfer in the ternary intercalated graphite beta-KS0.25C3.

The electronic structure of the ternary intercalated graphite beta-KS(0.25)C3 is studied by means of a first-principles density functional theory approach. The nature of the partially filled bands is analyzed, and the K sublayers of the intercalate are shown to have an important contribution to the Fermi surface. This K-based contribution confers a sizable three-dimensional character to the conductivity even if considerably less than that for the related binary KC8. The electronic structure of beta-KS(0.25)C3 differs noticeably from that of the related ternary compound, KH(x)C4. The charge transfer is analyzed, and a way to evaluate it, which can be used in general for intercalated graphites, is proposed. The charge transfer per C atom in this ternary material is shown to be smaller than that in the KC8 binary compound despite a more favorable stoichiometry ratio between K and C.

Journal Article↗
PubMed2000

Electronic structures of M21S8 (M = Nb, Zr) and (M,M')21S8 (M, M' = Hf, Ti; Nb, Ta) phases and reasons for variations in the metal site occupations.

The electronic structures of binary M21S8 (M = Nb, Zr) and isostructural ternary (M,M')21S8 (M, M' = Hf, Ti; Nb, Ta) phases have been studied by means of extended Hückel tight-binding band structure calculations. For the valence electron concentration in the binary group 5 metal phase Nb21S8, metal-metal bonding is optimized whereas, in the isostructural group 4 metal phase Zr21S8, metal-metal bonding levels exist above the Fermi level. However, the electronic structure analysis suggests a stable structure for M21S8 phases with group 4 metals and that (M,M')21S8 phases with mixed group 4 and group 5 metals, even if not yet reported, could well exist. In the ternary phase Nb6.9Ta14.1S8, a linear relationship exists between the magnitude of the metal-metal bonding capacity (as expressed by the total metal-metal Mulliken overlap population) of each crystallographically independent metal site and the occupation of the site with the heavier metal (i.e., the element with the greater bonding capability). The situation is quite more complex in Hf7.5Ti13.5S8, where the metal-metal bonding capacity of each site, differences in electronegativity between Ti and Hf, and site volume arguments must be taken into account to understand the metal site occupation.

Journal Article↗
PubMed2002

Electronic structure and its relation to function in copper proteins.

Spectroscopic and theoretical investigations of the geometric and electronic structures of mononuclear and binuclear copper sites in proteins help in understanding the contributions of these proteins to biological electron transfer. Spectroscopically calibrated density functional theory calculations, which give reasonable bonding descriptions in both ground- and excited-states, define the role of the protein in determining the geometric and electronic structure of the active site.

Binding Sites↗
PubMed2004

Terminal ligand influence on the electronic structure and intrinsic redox properties of the [Fe4S4]2+ cubane clusters.

We used photoelectron spectroscopy (PES) to study how the terminal ligands influence the electronic structure and redox properties of the [4Fe-4S] cubane in several series of ligand-substituted analogue complexes: [Fe(4)S(4)Cl(4-x)(CN)(x)](2-), [Fe(4)S(4)Cl(4-x)(SCN)(x)](2-), [Fe(4)S(4)Cl(4-x)(OAc)(x)](2-), [Fe(4)S(4)(SC(2)H(5))(4-x)(OPr)(x)](2-), and [Fe(4)S(4)(SC(2)H(5))(4-x)Cl(x)](2-) (x = 0-4). All the ligand-substituted complexes gave similar PES spectral features as the parents, suggesting that the mixed-ligand coordination does not perturb the electronic structure of the cubane core significantly. The terminal ligands, however, have profound effects on the electron binding energies of the cubane and induce significant shifts of the PES spectra, increasing in the order SC(2)H(5)(-) --> Cl(-) --> OAc(-)/OPr(-) --> CN(-) --> SCN(-). A linear relationship between the electron binding energies and the substitution number x was observed for each series, indicating that each ligand contributes independently and additively to the total binding energy. The electron binding energies of the gaseous complexes represent their intrinsic oxidation energies; the observed linear dependence on x is consistent with similar observations on the redox potentials of mixed-ligand cubane complexes in solution. The current study reveals the electrostatic nature of the interaction between the [4Fe-4S] cubane core and its coordination environment and provides further evidence for the electronic and structural stability of the cubane core and its robustness as a structural and functional unit in Fe-S proteins.

Electrochemistry↗
PubMed2005

Spectroscopic and computational studies of Ni superoxide dismutase: electronic structure contributions to enzymatic function.

Ni-containing superoxide dismutase (NiSOD) is the most recently discovered member of the class of metalloenzymes that detoxify the superoxide radical in aerobic organisms. In this study, we have employed a variety of spectroscopic and computational methods to probe the electronic structure of the NiSOD active site in both its oxidized (NiSOD(ox), possessing a low-spin (S = (1)/(2)) Ni(3+) center) and reduced (NiSOD(red), containing a diamagnetic Ni(2+) center) states. Our experimentally validated computed electronic-structure description for NiSOD(ox) reveals strong sigma-bonding interactions between Ni and the equatorial S/N ligands, which give rise to intense charge-transfer transitions in the near-UV region of the absorption spectrum. Resonance Raman (rR) spectra obtained with laser excitation in this region exhibit two features at 349 and 365 cm(-)(1) that are assigned to Ni-S(Cys) stretching modes. The NiSOD(red) active site also exhibits a high degree of metal-ligand bond covalency as well as filled/filled pi-interactions between Ni and S/N orbitals, which serve to adjust the redox potential of the Ni(2+) center. Comparison of our computational results for NiSOD(red) with those obtained in parallel studies of synthetic [NiS(2)N(2)] complexes reveals that the presence of an anionic N-donor ligand is crucial for promoting metal-based (versus S-based) oxidation of the active site. The implications of our electronic-structure descriptions with respect to the function of NiSOD are discussed, and a comparison of M-S(Cys) bonding in NiSOD and other metalloenzymes with sulfur ligation is provided.

Binding Sites↗
PubMed2004

Density functional theory and ab initio studies of geometry, electronic structure and vibrational spectra of novel benzothiazole and benzotriazole herbicides.

The ground-state geometries, electronic structures and vibrational wavenumbers of S-1,3-benzothiazolyl-4-bromobenzenecarbothioate and S-(5,7-dimethyl-3H-4lambda-5-[1,2,4]triazolo[1,5-a]pyridinyl)4-chlorobenzenecarbothioate were studied by DFT-B3LYP, BLYP and ab initio RHF method with different basis sets. The comparison was performed for optimized geometries, thermodynamic parameters and electronic structures at different levels of theory. Because of the larger repulsion effect in triazole ring, the vibrational wavenumbers of skeleton vibration of triazole ring are significantly lower than that of thiazole ring.

Benzothiazoles↗
PubMed2006

Electronic structure of the [MNH2]+ (M = Sc-Cu) complexes.

B3LYP geometry optimizations for the [MNH2]+ complexes of the first-row transition metal cations (Sc+-Cu+) were performed. Without any exception the ground states of these unsaturated amide complexes were calculated to possess planar geometries. CASPT2 binding energies that were corrected for zero-point energies and including relativistic effects show a qualitative trend across the series that closely resembles the experimental observations. The electronic structures for the complexes of the early and middle transition metal cations (Sc+-Co+) differ from the electronic structures derived for the complexes of the late transition metal cations (Ni+ and Cu+). For the former complexes the relative higher position of the 3d orbitals above the singly occupied 2p(pi) HOMO of the uncoordinated NH2 induces an electron transfer from the 3d shell to 2p(pi). The stabilization of the 3d orbitals from the left to the right along the first-row transition metal series causes these orbitals to become situated below the HOMO of the NH2 ligand for Ni+ and Cu+, preventing a transfer from occurring in the [MNH2]+ complexes of these metal cations. Analysis of the low-lying states of the amide complexes revealed a rather unique characteristic of their electronic structures that was found across the entire series. Rather exceptionally for the whole of chemistry, pi-type interactions were calculated to be stronger than the corresponding sigma-type interactions. The origin of this extraordinary behavior can be ascribed to the low-lying sp2 lone pair orbital of the NH2 ligand with respect to the 3d level.

Journal Article↗
PubMed2003

Interpretation of the magnetic structures of Cu2Te2O5X2 (X = Cl, Br) and Ca3.1Cu0.9RuO6 on the basis of electronic structure considerations: cases for strong super-superexchange interactions involving Cu2+ ions.

For super-superexchange interactions between Cu(2+) ions, a qualitative rule was formulated to assess their strengths based on the geometrical parameters of the exchange paths. Spin dimer analysis was carried out for Cu(2)Te(2)O(5)X(2) (X = Cl, Br) and Ca(3.1)Cu(0.9)RuO(6) to evaluate the relative strengths of their superexchange and super-superexchange interactions. The strongest antiferromagnetic interactions in Cu(2)Te(2)O(5)X(2) (X = Cl, Br) are given by the super-superexchange interactions involving the most linear Cu-X.X-Cu paths between tetrahedral clusters Cu(4)O(8)X(4) along the (a +/- b)-directions. The adjacent CuRuO(6) chains of Ca(3.1)Cu(0.9)RuO(6) are antiferromagnetically coupled through the most linear Cu-O.O-Cu paths along the direction perpendicular to the plane of the CuRu zigzag chain. The spin lattices of Cu(2)Te(2)O(5)X(2) and Ca(3.1)Cu(0.9)RuO(6) deduced from our spin dimer analysis are consistent with the available magnetic data. The spin lattice of a magnetic solid should be determined on the basis of appropriate electronic structure considerations.

Journal Article↗
PubMed2004

Orientation-dependent C60 electronic structures revealed by photoemission spectroscopy.

We observe, with angle-resolved photoemission, a dramatic change in the electronic structure of two C60 monolayers, deposited, respectively, on Ag (111) and (100) substrates, and similarly doped with potassium to half filling of the C60 lowest unoccupied molecular orbital. The Fermi surface symmetry, the bandwidth, and the curvature of the dispersion at Gamma point are different. Orientations of the C60 molecules on the two substrates are known to be the main structural difference between the two monolayers, and we present new band-structure calculations for some of these orientations. We conclude that orientations play a key role in the electronic structure of fullerides.

Journal Article↗
PubMed1977

Visual chromophore electronic structure.

The implications that recent work on the electronic structure of polyenes have for the low lying electronic states of retinal reviewed and a very simple model for the diffusenesss of the absorption spectra of visual chromophores is presented.

Chemical Phenomena↗
PubMed2003

Electronic structures of Ascaris trypsin inhibitor in solution.

The electronic structures of Ascaris trypsin inhibitor in solution are obtained by the first-principles, all-electron, ab initio calculation using the self-consistent cluster-embedding (SCCE) method. The inhibitor, made up of 62 amino acid residues with 912 atoms, has two three-dimensional solution structures: 1ata and 1atb. The calculated ground-state energy of structure 1atb is lower than that of structure 1ata by 6.12 eV. The active sites are determined and explained: only structure 1atb has a N terminal at residue ARG+31. This shows that the structure 1atb is the stable and active form of the inhibitor, which is in agreement with the experimental results. The calculation reveals that some parts of the inhibitor can be easily changed while the inhibitor's biological activity may be kept. This kind of information may be helpful in fighting viruses such as AIDS, SARS, and flu, since these viruses have higher variability. The calculation offers an independent theoretical estimate of the precision of structure determination.

Animals↗
PubMed2002

Self-consistent average-atom scheme for electronic structure of hot and dense plasmas of mixture.

An average-atom model is proposed to treat the electronic structures of hot and dense plasmas of mixture. It is assumed that the electron density consists of two parts. The first one is a uniform distribution with a constant value, which is equal to the electron density at the boundaries between the atoms. The second one is the total electron density minus the first constant distribution. The volume of each kind of atom is proportional to the sum of the charges of the second electron part and of the nucleus within each atomic sphere. By this way, one can make sure that electrical neutrality is satisfied within each atomic sphere. Because the integration of the electron charge within each atom needs the size of that atom in advance, the calculation is carried out in a usual self-consistent way. The occupation numbers of electron on the orbitals of each kind of atom are determined by the Fermi-Dirac distribution with the same chemical potential for all kinds of atoms. The wave functions and the orbital energies are calculated with the Dirac-Slater equations. As examples, the electronic structures of the mixture of Au and Cd, water (H2O), and CO2 at a few temperatures and densities are presented.

Journal Article↗
PubMed2004

Theoretical study of the surface energy and electronic structure of pyrite FeS2 (100) using a total-energy pseudopotential method, CASTEP.

The geometric and electronic structures of FeS(2) (100) surface have been studied by a quantum-mechanical calculation using a total-energy pseudopotential code, CASTEP. The (100) surface is very stable and does not give any significant geometric relaxation. The electronic structure of FeS(2) (100) surface is characterized by the appearance of new native surface states in the bulk band gap, which correspond to antibonding mixed Fea-Ssp(3) states. These surface states play an important role as mediators of electron transfer on both anodic and cathodic sites in the incipient oxidation of pyrite. Moreover, the (100) surface has small band gaps and shows some metallic character. It is predicted that the rate of cathodic reductive reaction of O(2) in the incipient oxidation of pyrite is much faster than previously considered. The transport of electrons from the anodic sites to the cathodic sites on the (100) surface is faster and hole injection of anodic sites is not the rate-determining step. So we can deduce that the rate-determining step of incipient oxidation for pyrite consists of both electron transfer of pyrite/aqueous O(2) interface and the splitting of H(2)O.

Journal Article↗
PubMed2004

Effects of axial methionine coordination on the in-plane asymmetry of the heme electronic structure of cytochrome c.

The paramagnetic susceptibility ( chi) tensors of the oxidized forms of thermophile Hydrogenobacter thermophilus cytochrome c(552) (Ht cyt c(552)) and a quintuple mutant (F7A/V13 M/F34Y/E43Y/V78I; qm) of mesophile Pseudomonas aeruginosa cytochrome c(551) (Pa cyt c(551)) have been determined on the basis of the redox-dependent (1)H NMR shift changes of the main-chain NH and C(alpha)H proton resonances of non-coordinated amino acid residues and the NMR structures of the reduced forms of the corresponding proteins (J. Hasegawa, T. Yoshida, T. Yamazaki, Y. Sambongi, Y. Yu, Y. Igarashi, T. Kodama, K. Yamazaki, Y. Kyogoku, Y. Kobayashi (1998) Biochemistry 37:9641-9649; J. Hasegawa, S. Uchiyama, Y. Tanimoto, M. Mizutani, Y. Kobayashi, Y. Sambongi,Y. Igarashi (2000) J Biol Chem 275:37824-37828). From the chi tensors determined, we obtained the contact shifts for heme methyl proton resonances, which provided the heme electronic structures of the oxidized forms of Ht cyt c(552) and qm. We also characterized the heme electronic structure of the cyanide adducts of the proteins, where the axial Met was replaced by an exogenous cyanide ion, through the analysis of (1)H NMR spectra. The results indicated that the heme electronic structures of both the proteins in their oxidized forms with axial His and Met coordination are largely different to each other, while those in their cyanide adducts are similar to each other. These results demonstrated that the orientation of the axial Met sulfur lone pair, with respect to heme, predominantly contributes to the spin delocalization into the porphyrin-pi system of heme in the oxidized proteins with axial His and Met coordination.

Cytochromes c↗
PubMed2003

Electronic structure and reactivity of high-spin iron--alkyl- and--pterinperoxo complexes.

The spectroscopic properties and electronic structure of the four-coordinate high-spin [FeIII(L3)(OOtBu)]+ complex (1; L3 = hydrotris(3-tert-butyl-5-isopropyl-1-pyrazolyl)borate; tBu = tert-butyl) are investigated and compared to the six-coordinated high-spin [Fe(6-Me3TPA)(OHx)(OOtBu)]x+ system (TPA = tris(2-pyridylmethyl)amine, x = 1 or 2) studied earlier [Lehnert, N.; Ho, R. Y. N.; Que, L., Jr.; Solomon, E. I. J. Am. Chem. Soc. 2001, 123, 12802-12816]. Complex 1 is characterized by Raman features at 889 and 830 cm-1 which are assigned to the O-O stretch (mixed with the symmetric C-C stretch) and a band at 625 cm-1 that corresponds to nu(Fe-O). The UV-vis spectrum shows a charge-transfer (CT) transition at 510 nm from the alkylperoxo pi v* (v = vertical to C-O-O plane) to a d orbital of Fe(III). A second CT is identified from MCD at 370 nm that is assigned to a transition from pi h* (h = horizontal to C-O-O plane) to an Fe(III) d orbital. For the TPA complex the pi v* CT is at 560 nm while the pi h* CT is to higher energy than 250 nm. These spectroscopic differences between four- and six-coordinate Fe(III)-OOR complexes are interpreted on the basis of their different ligand fields. In addition, the electronic structure of Fe-OOPtn complexes with the biologically relevant pterinperoxo ligand are investigated. Substitution of the tert-butyl group in 1 by pterin leads to the corresponding Fe(III)-OOPtn species (2), which shows a stronger electron donation from the peroxide to Fe(III) than 1. This is related to the lower ionization potential of pterin. Reduction of 2 by one electron leads to the Fe(II)-OOPtn complex (3), which is relevant as a model for potential intermediates in pterin-dependent hydroxylases. However, in the four-coordinate ligand field of 3, the additional electron is located in a nonbonding d orbital of iron. Hence, the pterinperoxo ligand is not activated for heterolytic cleavage of the O-O bond in this system. This is also evident from the calculated reaction energies that are endothermic by at least 20 kcal/mol.

Alkynes↗
PubMed2005

Geometric and electronic structure of the heme-peroxo-copper complex [(F8TPP)FeIII-(O22-)-CuII(TMPA)](ClO4).

The geometric and electronic structure of the untethered heme-peroxo-copper model complex [(F(8)TPP)Fe(III)-(O(2)(2)(-))-Cu(II)(TMPA)](ClO(4)) (1) has been investigated using Cu and Fe K-edge EXAFS spectroscopy and density functional theory calculations in order to describe its geometric and electronic structure. The Fe and Cu K-edge EXAFS data were fit with a Cu...Fe distance of approximately 3.72 A. Spin-unrestricted DFT calculations for the S(T) = 2 spin state were performed on [(P)Fe(III)-(O(2)(2)(-))-Cu(II)(TMPA)](+) as a model of 1. The peroxo unit is bound end-on to the copper, and side-on to the high-spin iron, for an overall mu-eta(1):eta(2) coordination mode. The calculated Cu...Fe distance is approximately 0.3 A longer than that observed experimentally. Reoptimization of [(P)Fe(III)-(O(2)(2)(-))-Cu(II)(TMPA)](+) with a 3.7 A Cu...Fe constrained distance results in a similar energy and structure that retains the overall mu-eta(1):eta(2)-peroxo coordination mode. The primary bonding interaction between the copper and the peroxide involves electron donation into the half-occupied Cu d(z)2 orbital from the peroxide pi(sigma) orbital. In the case of the Fe(III)-peroxide eta(2) bond, the two major components arise from the donor interactions of the peroxide pi*(sigma) and pi*(v) orbitals with the Fe d(xz) and d(xy) orbitals, which give rise to sigma and delta bonds, respectively. The pi*(sigma) interaction with both the half-occupied d(z)2 orbital on the copper (eta(1)) and the d(xz) orbital on the iron (eta(2)), provides an effective superexchange pathway for strong antiferromagnetic coupling between the metal centers.

Copper↗