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PubMed2005

Evolution of the geometrical and electronic structures of Gan(n=2-26) clusters: a density-functional theory study.

Density-functional theory with generalized gradient approximation for the exchange-correlation potential has been used to calculate the lowest-energy geometries and electronic structure of neutral gallium clusters containing up to 26 atoms. Harmonic vibrational frequency analysis is undertaken to assure that the lowest-energy geometries are real local minima. With increasing cluster size, we find that the gallium clusters tend to adopt compact structures. The structures comprise triangular units that connect each other with different dihedral angles. The lowest-energy structure can be obtained by capping an atom on the structure of smaller one. The capping site occurs at a site where interactions with more atoms are available. The binding energy evolves monotonically with size, but Ga(8), Ga(14), and Ga(20) exhibit particularly higher stability. Except Ga(2) and Ga(4), all even-numbered gallium clusters we studied are closed-shell singlet states with a substantial highest occupied and lowest unoccupied molecular orbitals gap. The odd-numbered clusters are open shell with a small gap. The size dependence of cluster's ionization potentials and electron affinities is discussed and compared with available experiment.

Journal Article↗
PubMed2004

The interdependence of defects, electronic structure and surface chemistry.

In this article we present three diverse applications of first-principles simulations to problems of materials chemistry and chemical physics. Their common characteristic is that they are essentially problems of the relationships among atomic structures and the properties they promote in real materials and real applications. The studies are on transition-metal oxide surface chemistry, the reactivity and electronic structure of sp(2)-bonded carbon systems, and defects and electrochromic properties in WO(3). In these demanding applications we must have concern for how realistic our model systems are and how well current implementations of DFT perform, and we comment on both.

Journal Article↗
PubMed2005

Ab initio investigation of the electronic structure and bonding of the HC(N2)x(+) and HC(CO)x(+) cations, x = 1, 2.

Employing the coupled-cluster approach and correlation consistent basis sets of triple and quadruple cardinality, we have investigated the electronic structure and bonding of the HC(N2)x(+) and HC(CO)x(+), x = 1, 2, molecular cations. We report geometries, binding energies and potential energy profiles. The ground states of HC(N2)+, HC(CO)+ and HC(N2)2(+), HC(CO)2(+) are of 3sigma- and 1A1 symmetries, respectively. All four charged species are well bound with binding energies ranging from 81 [HC(N2)+ (X3sigma-) --> CH+(a3pi) + N2(X1sigma(g)+)] to 178 [HC(CO)2(+)(X1A1) --> CH+(X1sigma+) + 2CO(X1sigma+)] kcal/mol. It is our belief that the X1A1 states of HC(N2)2(+) and HC(CO)2(+) are isolable in the solid state if combined with appropriate counteranions.

Journal Article↗
PubMed2006

Electronic structure of binuclear mixed valence copper azacryptates derived from integrated advanced EPR and DFT calculations.

Binuclear, mixed valence copper complexes with a [Cu(+1)(.5), Cu(+1)(.5)] redox state and S = (1)/(2) can be stabilized with rigid azacryptand ligands. In this system the unpaired electron is delocalized equally over the two copper ions, and it is one of the very few synthetic models for the electron mediating Cu(A) site of nitrous oxide reductase and cytochrome c oxidase. The spatial and electronic structures of the copper complex in frozen solution were obtained from the magnetic interactions, namely the g-tensor and the (63,65)Cu, (14)N, (2)H, and (1)H hyperfine couplings, in combination with density functional theory (DFT) calculations. The magnetic interactions were determined from continuous wave (CW) electron paramagnetic resonance (EPR), pulsed electron nuclear double resonance (ENDOR), two-dimensional TRIPLE, and hyperfine sublevel correlation spectroscopy (HYSCORE) carried out at W-band or/and X-band frequencies. The DFT calculated g and Cu hyperfine values were in good agreement with the experimental values showing that the structure in solution is indeed close to that of the optimized structure. Then, the DFT calculated hyperfine parameters were used as guidelines and starting points in the simulations of the various experimental ENDOR spectra. A satisfactory agreement with the experimental results was obtained for the (14)N hyperfine and quadrupole interactions. For (1)H the DFT calculations gave good predictions for the hyperfine tensor orientations and signs, and they were also successful in reproducing trends in the magnitude of the various proton hyperfine couplings. These, in turn, were very useful for ENDOR signals assignments and served as constraints on the simulation parameters.

Journal Article↗
PubMed2004

Electronic structure and photochemistry of squaraine dyes: basic theoretical analysis and direct detection of the photoisomer of a symmetrical squarylium cyanine.

The photoisomerization kinetics of a squaraine dye has been the object both of experimental investigation and of interpretation in the framework of a qualitative theoretical model formulated by the aid of simple HMO calculations and orbital symmetry considerations. Such a model has first confirmed that the electronic structure and the spectroscopic properties of symmetrical squaraines are related to those of the parent cyanines, with ketocyanines as intermediate systems. Extension of the approach to structures twisted by 90[degree] about a polymethine bond has then provided insight into the electronic aspects and the mechanism of the photoisomerization of the squaraine under study. The reaction, previously indirectly investigated by fluorescence analysis, has been directly monitored by laser flash photolysis. These experiments indicate that, while photoisomerization is likely the main radiationless decay route from the spectroscopic minimum of the lowest excited singlet state (S(1)), the cis photoisomer is produced with only a 1% yield, likely because of an unfavourable cis/trans branching ratio from the perpendicular minimum of the S(1)-state potential energy surface. In contrast with what found for symmetrical cyanines, an increase in the solvent polarity was found to accelerate both the direct, excited-state reaction and, to a much larger extent, the ground-state back-isomerization. Such observations are consistent with predictions of the theoretical model and provide a clue for the identification of the isomerization coordinate.

Journal Article↗
PubMed2002

Electronic structure of MgB2 from angle-resolved photoemission spectroscopy.

The first angle-resolved photoemission spectroscopy results from MgB2 single crystals are reported. Along the GammaK and GammaM directions, we observed three distinct dispersive features approaching the Fermi energy. These can be assigned to the theoretically predicted sigma (B 2p(x,y)) and pi (B 2p(z)) bands. In addition, a small parabolic-like band is detected around the Gamma point, which can be attributed to a surface-derived state. The overall agreement between our results and the band calculations suggests that the electronic structure of MgB2 is of a conventional nature, thus implying that electron correlations are weak and may be of little importance to superconductivity in this system.

Journal Article↗
PubMed2005

Where is the spin? Understanding electronic structure and g-tensors for ruthenium complexes with redox-active quinonoid ligands.

Understanding the bonding in transition metal complexes with redox-active ligands is a major challenge, for example in redox catalysis or in bioinorganic chemistry. In this work, electronic g-tensors, spin-density distributions, and electronic structure have been studied by different density functional methods for an extended series of complexes [Ru(acac)2(L)]n (n = -1, 0, +1; L = redox-active o-quinonoid ligand). Comparison is made with experimental g-tensors and g-tensor-based oxidation-state assignments for a number of experimentally studied examples, using both gradient-corrected (BP86) and hybrid functionals (B3LYP, BHLYP) representing a range of exact-exchange admixtures. Reasonable, albeit not perfect, agreement with experimental g-tensors is obtained in one-component DFT calculations with hybrid functionals. Analyses of spin densities confirm the assignment of the cationic complexes as predominantly d5-Ru(III) with a neutral quinonoid ligand. However, this conclusion is obtained only after inclusion of the appreciable spin polarization of the unrestricted determinant, while the singly occupied molecular orbital (SOMO) is localized more on the acac ligands. The anionic complexes turn out to be approximately halfway between a d6-Ru(II)/semiquinone and a d5-Ru(III)/catecholate formulation, but again only after taking into account the extensive spin polarization. Even the previous assignment of the neutral parent systems as d5-Ru(III)/semiquinone is not accurate, as a d6-Ru(II)/quinone resonance structure contributes to some extent. Very unusual trends in the spin contamination of the Kohn-Sham determinant with increasing exact-exchange admixture in some of the cationic complexes have been traced to an interplay between spin delocalization and spin polarization.

Electrons↗
PubMed2005

Registering the Amica electronic structure code in the extensible computational chemistry environment.

We describe the integration and use of the Amica software package ("Atoms & Molecules In Chemical Accuracy") within the Extensible Computational Chemistry Environment (Ecce). Amica is capable of accurately solving the electronic Schrodinger equation of small atoms and molecules using terms that are linear in the interelectronic distances, r(12), on multireference level of theory, but it requires expert knowledge to configure and execute its algorithms. Ecce is a comprehensive suite of tools that support the computational chemistry research processes of computation setup, execution, and analysis through a convenient graphical user interface. Additionally, Ecce was architected with mechanisms to integrate alternative electronic structure codes. The successful integration of Amica within Ecce validates the architecture of the latter and brings the high-accuracy capabilities of Amica to a wider audience.

Journal Article↗
PubMed2001

Electronic structure of carbon nanocones.

Topology related changes in the local density of states near the apex of carbon nanocones are investigated using both tight-binding and ab initio calculations. Sharp resonant states are found to dominate the electronic structure in the region close to the Fermi energy. The strength and the position of these states with respect to the Fermi level depend sensitively on the number and the relative positions of the pentagons constituting the conical tip. Carbon nanocones are thus proposed as good candidates for nanoprobes in scanning probe microscopy.

Journal Article↗
PubMed2006

13C NMR studies of the electronic structure of low-spin iron(III) tetraphenylchlorin complexes.

A series of low-spin six-coordinate (tetraphenylchlorinato)iron(III) complexes [Fe(TPC)(L)2]+/- (L = 1-MeIm, CN-, 4-CNPy, and (t)BuNC) have been prepared, and their (13)C NMR spectra have been examined to reveal the electronic structure. These complexes exist as the mixture of the two isomers with the (d(xy))2(d(xz), d(yz))3 and (d(xz), d(yz))4(d(xy))1 ground states. Contribution of the (d(xz), d(yz))4(d(xy))1 isomer has increased as the axial ligand changes from 1-MeIm, to CN(-) (in CD2Cl2 solution), CN- (in CD(3)OD solution), and 4-CNPy, and then to tBuNC as revealed by the meso and pyrroline carbon chemical shifts; the meso carbon signals at 146 and -19 ppm in [Fe(TPC)(1-MeIm)2]+ shifted to 763 and 700 ppm in [Fe(TPC)(tBuNC)2]+. In the case of the CN- complex, the population of the (d(xz), d(yz))4(d(xy))1 isomer has increased to a great extent when the solvent is changed from CD2Cl2 to CD3OD. The result is ascribed to the stabilization of the d(xz) and d(yz) orbitals of iron(III) caused by the hydrogen bonding between methanol and the coordinated cyanide ligand. Comparison of the 13C NMR data of the TPC complexes with those of the TPP, OEP, and OEC complexes has revealed that the populations of the (d(xz), d(yz))4(d(xy))1 isomer in TPC complexes are much larger than those in the corresponding TPP, OEC, and OEP complexes carrying the same axial ligands.

Carbon Isotopes↗
PubMed1994

Site-specific mutagenesis of the reaction centre from Rhodobacter sphaeroides studied by Fourier transform Raman spectroscopy: mutations at tyrosine M210 do not affect the electronic structure of the primary donor.

The effects of mutation of residue tyrosine M210 on the primary donor bacteriochlorophylls have been investigated by near infrared FT-Raman spectroscopy in reaction centres purified from an antenna-deficient strain of Rhodobacter sphaeroides. We find that mutation at the M210 position does not significantly perturb the distribution of the unpaired electron over the pair of bacteriochlorophyll molecules which constitute the primary donor radical cation. We conclude, therefore, that the effects of mutation of tyrosine M210 on the rate and asymmetry of primary electron transfer in reaction centres cannot be ascribed to a change in the electronic structure of the primary donor.

Bacteriochlorophylls↗
PubMed1980

1H-NMR studies of the coordination geometry at the heme iron and the electronic structure of the heme group in cytochrome c-552 from Euglena gracilis.

The 1H-NMR lines of heme c in reduced and oxidized cytochrome c-552 from Euglena gracilis were individually assigned and the coordination geometry of the axial ligands was investigated. The electronic structure of the heme and the chirality of the axially bound methionine were found to be of the same type as in mammalian cytochrome c, but different from cytochrome c-551 from Pseudomonas aeruginosa. These results provide additional support for a previously proposed correlation between the chirality of attachment of the axial methionine and the electronic wave functions in oxidized cytochromes of the c type. Comparison of mammalian cytochrome c, cytochrome c-551 and cytochrome c-552 indicates that the chirality of the axially bound methionine is not linked with the evolutionary increase of the polypeptide chain length.

Animals↗
PubMed2004

Effect of meta electron-donating groups on the electronic structure of substituted phenyl nitrenium ions.

Density functional theory (UB3LYP/6-31G(d,p)) was used to determine substituent effects on the singlet-triplet-state energy gap for 21 meta-substituted phenylnitrenium ions. It was found that strongly electron-donating substituents stabilize the triplet state relative to the singlet state. With sufficiently strong meta electron donors (e.g., m,m'-diaminophenylnitrenium ion) the triplet is predicted to be the ground state. Analysis of equilibrium geometries, Kohn-Sham orbital distributions, and Mulliken spin densities for the triplet states of this series of nitrenium ions leads to the conclusion that there are two spatially distinct types of low-energy triplet states. Simple arylnitrenium ions such as phenylnitrenium ions as well as those having electron-withdrawing or weakly donating meta substituents have lowest-energy triplet states that are n,pi in nature. That is, one singly occupied molecular orbital is orthogonal to the plane of the phenyl ring and one is coplanar. These n,pi triplets are generally characterized by large ArNH bond angles (ca. 130-132 degrees ) and an NH bond that is perpendicular to the plane of the phenyl ring. In contrast, meta donor arylnitrenium ions have a lowest-energy triplet state best described as pi,pi. That is, both singly occupied molecular orbitals are orthogonal to the aromatic ring. Such pi,pi states are characterized by NH bonds that are coplanar with the phenyl ring and have ArNH bond angles that are more acute (ca. 110-111 degrees ). These triplet nitrenium ions have electronic structures analogous to those of meta-benzoquinodimethane derivatives.

Journal Article↗
PubMed2006

Molecular and electronic structure in NaCl electrolytes of varying concentration: identification of spectral fingerprints.

Near edge x-ray absorption spectra at the Na K edge in aqueous NaCl electrolytes are presented as a function of concentration. The spectra are modeled by electronic structure calculations. We find and identify the orbital origin of two spectral fingerprints with sensitivity to the Na+-H2O distance and the Na+-Cl- distance in the electrolyte. Interionic interaction is found to be crucial for the description of the electrolytes at high concentrations.

Journal Article↗
PubMed2001

Atomic and electronic structures of N-incorporated Si oxides.

We present first-principles total-energy calculations on the N-incorporated Si oxides, regarded as a replacement for conventional SiO2 in device technology. We investigate the energetics, charge states, and electronic structures for various bond configurations around N. While they remain in the N-incorporated structures, the charge trap states, responsible for leakage current in SiO2, are effectively removed from the energy gap in the H-terminated structures. This shows that improvement in the electrical reliabilities of Si oxynitride films is originated not from N incorporation itself, but from the coexistence of N and H.

Journal Article↗
PubMed2006

Gas-phase generation and electronic structure investigation of chlorosulfanyl thiocyanate, ClSSCN.

The chlorosulfanyl thiocyanate molecule, ClSSCN, was generated in the gas phase through heterogeneous reaction of SCl2 on the surface of finely powdered AgSCN for the first time. The reaction products were detected and characterized in situ by ultraviolet photoelectron and photoionization mass spectrometry. The molecular geometry and electronic structures of ClSSCN were investigated by a combination of PES experiment and theoretical calculations with the density functional theory and ab initio methods. It was found that the outermost electrons of ClSSCN reside in the Cl-S antibonding pi orbital, predominantly localized on the sulfur atom, and the experimental first vertical ionization potential of ClSSCN is 10.20 eV. The dominant fragment SSCN+ in the mass spectrum indicates that the ClSSCN cation prefers the dissociation of the Cl-S bond.

Journal Article↗
PubMed2006

Conductance maps by electrochemical tunneling spectroscopy to fingerprint the electrode electronic structure.

We describe a methodology to perform reliable tunneling spectroscopy in electrochemical media. Sequential in situ tunneling spectra are recorded while the electrochemical potential of the electrode is scanned. Spectroscopic data are presented as conductance maps or conductograms that show the in situ electronic structure of an electrode surface while it undergoes an electrochemical reaction. The conductance map or conductogram represents the redox fingerprint of an electrode/liquid interface in a specific medium and can serve to predict its electrochemical behavior in a quantitative energy scale. The methodology is validated studying the reversible oxidation and passivity of an iron electrode in borate buffer, and we describe the main quantitative information that can be extracted concerning the semiconducting properties of the Fe passive film. This methodology is useful to study heterogeneous catalysis, electrochemical sensing and bioelectronic systems.

Electrochemistry↗
PubMed2006

Fluorophore(s) appended fullerene dyads and triads for probing photoinduced energy transfer: syntheses, electronic structure, and fluorescence studies.

Fullerene, C(60) was functionalized to possess one or two fluorophore entities. The fluorophore-fullerene dyads thus synthesized contain either a naphthalene, pyrene, or fluorene entity while the triads contain either a pyrene or fluorene entity in addition to a naphthalene entity. The redox behavior of these dyads and triads were probed by cyclic voltammetric technique, while the geometry and electronic structures were deduced from ab initio B3LYP/3-21G(*) method. Steady-state emission studies revealed the occurrence of energy transfer from the singlet excited fluorophore to the fullerene entity in the case of the dyads while the occurrence of step-by-step sequential energy transfer is envisioned in the case of the triads. A better 'antenna-effect' owing to the extended range of excitation wavelength to induce energy transfer to the appended fullerene has been achieved in the case of the triads.

Computational Biology↗