Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “electronic structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6Linked to original sources
PubMed2005

Electronic structure and bonding in hydroxocobalamin.

The electronic structure of hydroxocobalamin (OHCbl) has been calculated by a density functional method, using the orthogonalized linear combination of the atomic orbitals method (OLCAO). The X-ray crystal structure has been determined from synchrotron X-ray diffraction data and the geometry determined was used in the calculations. Comparison with the recently reported electronic structures of cyanocobalamin (CNCbl), methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl) shows that Mulliken charges (Q*) and bond orders (BO) vary only on the axial fragment.

Cobamides↗
PubMed2003

A novel layered niobium oxychloride compound based on Nb2 pairs and Nb6 octahedral clusters: synthesis and crystal and electronic structures of Nb10Cl16O7.

The synthesis, single crystal structure determination, and electronic structure of Nb10Cl16O7, the first Nb6 oxychloride stabilized without countercation, are reported in this work. The crystal structure is very original since it consists of layers built up from both Nb6 octahedral clusters and Nb2 pairs. The Nb6Oi6Cli6Cla6 and Nb2(mu2-Cl)2Cl4O4 units form [Nb6Cli6Oi4O(i-i)(2/2)Cl(a-a)(4/2)Cla2]infinity infinite chains and [(Nb2(mu2-Cl)2O(2/2)Cl(4/2)O2)2]infinity double chains, respectively, that are interconnected by shared oxygen and chlorine ligands leading to layers. The cohesion of the three-dimensional structure (3D) is ensured by van der Waals contacts between layers that are randomly stacked along the [011] direction. Structural correlations between Nb10Cl16O7 and related Nb6 cluster oxyhalides, as well as NbOCl2 and NbCl4 containing Nb2 pairs, are discussed. DFT results show that among the 20 valence electrons involved in the metal-metal bonding states, 14 electrons belong to the octahedral Nb6Cli6Oi6Cla6 unit whereas the 6 others (i.e., 1.5 per Nb atom) participate in the bonding in the distorted [(Nb2(mu2-Cl)2O(2/2)Cl(4/2)O2)2]infinity double chains.

Journal Article↗
PubMed2006

Electronic structure analyses of BN network materials using high energy-resolution spectroscopy methods based on transmission electron microscopy.

Electronic structures of boron-nitride (BN) nanotubes and a BN cone-structure material were studied by using a high energy-resolution electron energy-loss spectroscopy (EELS) microscope. A trial of the whole electronic structure study of hexagonal BN (h-BN), which consists of flat BN honeycomb layers, was conducted by a combination of EELS and X-ray emission spectroscopy (XES) based on transmission electron microscopy (TEM) (TEM-EELS/XES). The pi and pi+sigma plasmon energies of BN nanotubes (BNT) were smaller than those of h-BN. The pi+sigma energy was explained by the surface plasmon excitation. The spectrum of a two-wall BNT of 2.7 nm in diameter showed a new spectral onset at 4 eV. The valence electron excitation spectra obtained from the tip region of the BN cone with an apex angle of 20 degrees showed similar intensity distribution with those of BNTs. The B K-shell electron excitation spectra obtained from the bottom edge region of the BN cone showed additional peak intensity when compared with those of h-BN and BNT. The B K-shell electron excitation spectra and B K-emission spectra of h-BN were compared with a result of a LDA band calculation. It showed that high symmetry points in the band diagram appear as peak and/or shoulder structures in the EELS and XES spectra. Interband transitions appeared in the imaginary part of the dielectric function of h-BN experimentally obtained were assigned in the band diagram. The analysis also presented that the LDA calculation estimated the bandgap energy smaller than the real material by an amount of 2 eV. Those results of TEM-EELS/XES analysis presented that high energy-resolution spectroscopy methods combined with TEM is a promising method to analyze whole electronic structures of nanometer scale materials.

Boron↗
PubMed2005

Electronic structure differences in ZrO2 vs HfO2.

Although ZrO2 and HfO2 are, for the most part, quite similar chemically, subtle differences in their electronic structures appear to be responsible for differing MO2/Si (M = Zr, Hf) interface stabilities. To shed light on the electronic structure differences between ZrO2 and HfO2, we have conducted joint experimental and theoretical studies. Because molecular electron affinities are a sensitive probe of electronic structure, we have measured them by conducting photoelectron spectroscopic experiments on ZrO2(-) and HfO2(-). The adiabatic electron affinity of HfO2 was determined to be 2.14 +/- 0.03 eV, and that of ZrO2 was determined to be 1.64 +/- 0.03 eV. Concurrently, advanced electronic structure calculations were conducted to determine electron affinities, vibrational frequencies, and geometries of these systems. The calculated CCSD(T) electron affinities of HfO2 and ZrO2 were found to be 2.05 and 1.62 eV, respectively. The molecular results confirm earlier predictions from solid state calculations that HfO2 is more ionic than ZrO2. The excess electron in MO2(-) occupies an sd-type hybrid orbital localized on the M atom (M = Zr, Hf). The structural parameters of ZrO2 and HfO2 and their vibrational frequencies were found to be very similar. Upon the excess electron attachment, the M-O bond length increases by ca. 0.04 A, the OMO angle increases by 2-4 degrees, and frequencies of all vibrational modes become smaller, with the stretching modes being shifted by 30-50 cm(-1) and the bending mode by 15-25 cm(-1). Together, these studies unveil significant differences in the electronic structures of ZrO2 and HfO2 but not in their structural or vibrational characteristics.

Journal Article↗
PubMed2006

Dependence of DNA electronic structure on environmental and structural variations.

We present experimental and theoretical evidence that varying the local environment and physical structure of dried DNA has a direct impact on its electronic structure. By preparing samples of DNA in various solutions, it was possible to alter the type of ions present during the production of the DNA samples. These variations resulted in differences in the local chemical environment of the dried DNA molecules. X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES) were used to probe the variations in the electronic structure of DNA samples. DFT calculations of a stack of 10 adenine (A)-thymine (T) nucleobase pairs show that slight structural variations in stacking height have a direct influence on the electronic structure and result in changes to the HOMO-LUMO gap. The effects of these differences in the local environment on the electronic structure are discussed and are related to the results of conductivity measurements of DNA.

DNA↗
PubMed2006

Photoelectron spectroscopy of the bis(dithiolene) anions [M(mnt)2]n- (M = Fe - Zn; n = 1, 2): changes in electronic structure with variation of metal center and with oxidation.

A detailed understanding of the electronic structures of transition metal bis(dithiolene) centers is important in the context of their interesting redox, magnetic, and optical properties. The electronic structures of the series [M(mnt)2]n- (M = Fe - Zn; mnt = 1,2-S2C2(CN)2; n = 1, 2) were examined by a combination of photodetachment photoelectron spectroscopy and density functional theory calculations, providing insights into changes in electronic structure with variation of the metal center and with oxidation. Significant changes were observed for the dianions [M(mnt)2]2- due to stabilization of the metal 3d levels from Fe to Zn and the transition from square-planar to tetrahedral coordination about the metal center (Fe-Ni, D(2h) --> Cu D2 --> Zn, D(2d). Changes with oxidation from [M(mnt)2]2- to [M(mnt)2]1- were largely dependent on the nature of the redox-active orbital in the couple [M(mnt)2](2-/1-). In particular, the first detachment feature for [Fe(mnt)2]2- originated from a metal-based orbital (Fe(II) --> Fe(III)) while that for [Fe(mnt)2]1- originated from a ligand-based orbital, a consequence of stabilization of Fe 3d levels in the latter. In contrast, the first detachment feature for both of [Ni(mnt)2]2- and [Ni(mnt)2]1- originated from the same ligand-based orbital in both cases, a result of occupied Ni 3d levels being stabilized relative those of Fe 3d and occurring below the highest energy occupied ligand-based orbital for both of [Ni(mnt)2]2- and [Ni(mnt)2]1- . The combined data illustrate the subtle interplay between metal- and ligand-based redox chemistry in these species and demonstrate changes in their electronic structures with variation of metal center, oxidation, and coordination geometry.

Journal Article↗
PubMed2001

Electronic structure studies of quinones and semiquinones: accurate calculation of spin densities and electron paramagnetic resonance parameters.

The application of electronic structure methods to the prediction of geometries, spin densities, and hyperfine couplings for biologically relevant quinones and semiquinones is reviewed. It is demonstrated that hybrid-type density functional methods are particularly suitable for such studies. Hydrogen bonding to the semiquinone oxygen by appropriate donors is shown to lead to a redistribution of spin density in the carbonyl group of the semiquinone. Experimental trends are well reproduced by the calculated values. Symmetric and asymmetric models of hydrogen bonding are modelled. It is shown that the symmetric models give good agreement with solution studies in vitro. The asymmetric models of hydrogen bonding give quite good agreement with values measured for in vivo semiquinones generated in the reaction centres of the purple photosynthetic bacterium, Rb sphaeroides, and also for the phyllosemiquinone free radical formed during electron transfer in Photosystem I of green plants. These recent advances in electronic structure calculations, in particular the applicability of density functional methods to the study of free radical properties, have opened up an exciting avenue for the complete characterisation of their electronic properties. In particular, the combination of experimental methods of electron paramagnetic resonance and such calculations should in future provide a clearer understanding of free radical chemistry in many areas of biology.

Electron Spin Resonance Spectroscopy↗
PubMed2005

Electronic structure of semiconducting nanotubes adsorbed on metal surfaces.

A total-energy electronic-structure calculation is performed to explore energetics and electronic structures of nanotubes adsorbed on metal surfaces. We find that the charge transfer from metal surfaces to the nanotubes takes place depending on both the electronic structures of the adsorbed nanotubes and the work functions of the metal surfaces. In addition, we also find a substantial hybridization between the electron states of metal atoms and those of the nanotubes, which results in the metal-induced inhomogeneous charge distribution in the nanotubes.

Journal Article↗
PubMed2000

19F NMR study of protein-induced rhombic perturbations on the electronic structure of the active site of myoglobin.

A novel C2-symmetric ring-fluorinated hemin, 13,17-bis(2-carboxyethyl)-2,8,12,18-tetramethyl-3,7-difluoroporphyrin atoiron(III), has been synthesized and was incorporated into sperm whale apomyoglobin to investigate protein-induced rhombic perturbations on the electronic structure of the active site of myoglobin (Mb) using 19F NMR spectroscopy. NMR signals for 19F atoms introduced as substituents on the present heme in ferrous low-spin and high-spin and ferric low-spin complexes have been observed and their shifts sharply reflect not only the electronic nature of the heme iron, but also in-plane asymmetry of the heme electronic structure. The two-fold symmetric electronic structure of the ring-fluorinated hemin is clearly manifested in the 19F and 1H NMR spectra of its dicyano complex. The chemical equivalence of the two fluorine atoms of the heme is removed in the active site of myoglobin and the splitting of the two 19F NMR signals provides a quantitative probe for characterizing the rhombic perturbation of the heme electronic structure induced by the heme-protein interaction. The in-plane asymmetry of heme electronic structures in carbon-monoxy and deoxy Mbs have been analyzed for the first time on the basis of the shift difference between the two 19F NMR signals of the heme and is interpreted in terms of iron-ligand binding and/or the orbital ground state of the heme. A potential utility of 19F NMR, combined with the use of a symmetric fluorinated hemin, in characterizing the heme electronic structure of myoglobin in a variety of iron oxidation, spin, and ligation states, is presented.

Animals↗
PubMed2005

Oxomolybdenum tetrathiolates with sterically encumbering ligands: modeling the effect of a protein matrix on electronic structure and reduction potentials.

The effect of sterically encumbering ligands on the electronic structure of oxomolybdenum tetrathiolate complexes was determined using a combination of electronic absorption and magnetic circular dichroism spectroscopies, complimented by DFT bonding calculations, to understand geometric and electronic structure contributions to reduction potentials. These complexes are rudimentary models for a redox-active metalloenzyme active site in a protein matrix and allow for detailed spectroscopic probing of specific oxomolybdenum-thiolate interactions that are directly relevant to Mo-S(cysteine) bonding in pyranopterin molybdenum enzymes. Data are presented for three para-substituted oxomolybdenum tetrathiolate complexes ([PPh4][MoO(p-SPhCONHCH3)4], [PPh4][MoO(p-SPhCONHC(CH2O(CH2)2CN)3)4], and [PPh4][MoO(p-SPhCONHC(CH2O(CH2)2COOCH2CH3)3)4]). The Mo(V/IV) reduction potentials of the complexes in DMF are -1213, -1251, and -1247 mV, respectively. The remarkably similar electronic absorption and magnetic circular dichroism spectra of these complexes establish that the observed reduction potential differences are not a result of significant changes in the electronic structure of the [MoOS4]- cores as a function of the larger ligand size. We provide evidence that these reduction potential differences result from the driving force for a substantial reorganization of the O-Mo-S-C dihedral angle upon reduction, which decreases electron donation from the thiolate sulfurs to the reduced molybdenum center. The energy barrier to favorable O-Mo-S-C geometries results in a reorganizational energy increase, relative to [MoO(SPh)4](-/2-), that correlates with ligand size. The inherent flexible nature of oxomolybdenum-thiolate bonds indicate that thiolate ligand geometry, which controls Mo-S covalency, could affect the redox processes of monooxomolybdenum centers in pyranopterin molybdenum enzymes.

Circular Dichroism↗
PubMed1999

Electronic structure and biological activity of steroids.

We present the analysis of the electronic structure for 31 steroids by using HeI UV photoelectron spectroscopy (UPS) and MO calculations. The electronic structure of molecules in the gas phase is related directly to steroid-receptor binding measurements. The results indicate that formally 'inert' sigma-skeleton plays a crucial role in diversifying the electronic structures of the title compounds ('ribbon-orbital effect'). This is an attempt to rationalize the biological activity of steroids (represented through steroid-receptor binding) by making direct correlation between spectroscopic and biological data.

Journal Article↗
PubMed2006

Second-order correction to perfect pairing: an inexpensive electronic structure method for the treatment of strong electron-electron correlations.

We have formulated a second-order perturbative correction for perfect-pairing wave functions [PP2] based on similarity-transformed perturbation techniques in coupled cluster theory. The perfect-pairing approximation is used to obtain a simple reference wave function which can qualitatively describe bond breaking, diradicals, and other highly correlated systems, and the perturbative correction accounts for the dynamical correlation. An efficient implementation of this correction using the resolution of the identity approximation enables PP2 to be computed at a cost only a few times larger than that of canonical MP2 for systems with hundreds of active electrons and tens of heavy atoms. PP2 significantly improves on MP2 predictions in various systems with a challenging electronic structure.

Journal Article↗
PubMed2005

A theoretical study on the electronic structures of TiO2: Effect of Hartree-Fock exchange.

The effects of the Fock exchange on the geometries and electronic structures of TiO2 have been investigated by introducing a portion of Hartree-Fock (HF) exchange into the traditional density functional. Our results indicate that the functional with 13% HF exchange can correctly predict the band gap and the electronic structures of rutile TiO2, and such an approach is also suitable to describe the structural and electronic properties of anatase and brookite phases. For the TiO2 (110) surfaces, although the surface relaxations are insensitive to the variation of HF exchange, there are larger effects on the positions of the occupied surface-induced states. When 13% HF exchange is employed, the predicted band gap of the perfect surface and position of defect state of the reduced surface are consistent with the experimental values. Moreover, the electronic structures of TiO2 (110) surface are carefully reexamined by using this hybrid density functional method.

Journal Article↗
PubMed2003

Spectroscopic studies of the Met182Thr mutant of nitrite reductase: role of the axial ligand in the geometric and electronic structure of blue and green copper sites.

A combination of spectroscopic methods and density functional calculations has been used to describe the electronic structure of the axial mutant (Met182Thr) of Rhodobacter sphaeroides nitrite reductase in which the axial methionine has been changed to a threonine. This mutation results in a dramatic change in the geometric and electronic structure of the copper site. The electronic absorption data imply that the type 1 site in the mutant is like a typical blue copper site in contrast to the wild-type site, which is green. Similar ligand field strength in the mutant and the wild type (from MCD spectra) explains the similar EPR parameters for very different electronic structures. Resonance Raman shows that the Cu-S(Cys) bond is stronger in the mutant relative to the wild type. From a combination of absorption, CD, MCD, and EPR data, the loss of the strong axial thioether (present in the wild-type site) results in an increase of the equatorial thiolate-Cu interaction and the site becomes less tetragonal. Spectroscopically calibrated density functional calculations were used to provide additional insight into the role of the axial ligand. The calculations reproduce well the experimental ground-state bonding and the changes in going from a green to a blue site along this coupled distortion coordinate. Geometry optimizations at the weak and strong axial ligand limits show that the bonding of the axial thioether is the key factor in determining the structure of the ground state. A comparison of plastocyanin (blue), wild-type nitrite reductase (green), and the Met182Thr mutant (blue) sites enables evaluation of the role of the axial ligand in the geometric and electronic structure of type 1 copper sites, which can affect the electron-transfer properties of these sites.

Bacterial Proteins↗
PubMed2004

Theoretical prediction of electronic structures of fully pi-conjugated zinc oligoporphyrins with curved surface structures.

A theoretical prediction of the electronic structures of fully pi-conjugated zinc oligoporphyrins with curved surface, ring, tube, and ball-shaped structures was conducted as the objective for the future development of triply meso-meso-, beta-beta-, and beta-beta-linked planar zinc oligoporphyrins. The excitation energies and oscillator strengths for the optimal ring and ball structures were calculated using the time-dependent density functional theory (DFT). Although there is an extremely small energy difference of < 0.1 eV between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the ring structure relative to the same-sized triply linked planar one, the Q and B bands of the former are smaller redshifted excitation energies and intensified oscillator strengths than those of the latter due to the structurally shortened effective pi-conjugated lengths for the electron transition. It is expected that the ball structure becomes an excellent electron acceptor and shows the highly redshifted Q' band in the near-IR region relative to the monomer. The minimum value of the HOMO-LUMO energy gaps of the infinite-length ring structures was estimated using periodic boundary conditions within the DFT, resulting in the metallic characters of both the tube structures with and without the spiral triply linked porphyrin array. The relation between the diameters and strain energies of the tube and ball structures was also examined. The present fused zinc porphyrins may become more colorful materials with new optelectronic properties including artificial photosynthesis than the carbon nanotubes and fullerenes when the axial coordinations of the central metal of porphyrins are functionally used.

Journal Article↗
PubMed2003

Probing the intrinsic electronic structure of the cubane [4Fe-4S] cluster: nature's favorite cluster for electron transfer and storage.

The cubane [4Fe-4S] is the most common multinuclear metal center in nature for electron transfer and storage. Using electrospray, we produced a series of gaseous doubly charged cubane-type complexes, [Fe4S4L4]2- (L = -SC2H5, -SH, -Cl, -Br, -I) and the Se-analogues [Fe4Se4L4]2- (L = -SC2H5, -Cl), and probed their electronic structures with photoelectron spectroscopy and density functional calculations. The photoelectron spectral features are similar among all the seven species investigated, revealing a weak threshold feature due to the minority spins on the Fe centers and confirming the low-spin two-layer model for the [4Fe-4S](2+) core and its "inverted level scheme". The measured adiabatic detachment energies, which are sensitive to the terminal ligand substitution, provide the intrinsic oxidation potentials of the [Fe4S4L4]2- complexes. The calculations revealed a simple correlation between the electron donor property of the terminal thiolate as well as the bridging sulfide with the variation of the intrinsic redox potentials. Our data provide intrinsic electronic structure information of the [4Fe-4S] cluster and the molecular basis for understanding the protein and solvent effects on the redox properties of the [4Fe-4S] active sites.

Iron↗
PubMed2005

Investigation of the scanning tunneling microscopy image, the stacking pattern, and the bias-voltage-dependent structural instability of 1,10'-phenanthroline molecules adsorbed on Au(111) in terms of electronic structure calculations.

A self-assembled monolayer of 1,10'-phenanthroline (phen) molecules on Au(111) was found to undergo a structural phase transition when the bias voltage is switched in scanning tunneling microscopy (STM) experiments (Phys. Rev. Lett. 1995, 75, 2376; Surf. Sci. 1997, 389, 19). The nature of two bright spots representing each phen molecule in the high-resolution STM images of phen molecules on Au(111) was identified by calculating the partial density plots for a monolayer of phen molecules adsorbed on Au(111) with tight-binding electronic structure calculations. The stacking pattern of chains of phen molecules on Au(111) was explained by studying the intermolecular interactions between phen molecules on the basis of first-principles electronic structure calculations for a phen dimer, (phen)(2). The structural instability of phen molecule arrangement caused by the bias-voltage switch was probed by estimating the adsorbate-surface interaction energy with the point-charge approximation for Au(111).

Journal Article↗
PubMed2006

Tuning the electronic structures of semiconducting SiC nanotubes by N and NHx (x=1,2) groups.

We investigate the stable configurations and electronic structures of silicon carbide nanotubes (SiCNTs) decorated by N and NHx (x=1,2) groups by using first-principles calculations. We find that these groups can be chemically incorporated into the network of SiCNTs in different ways, accompanied with the formation of N-C and N-Si bonds. The adsorbing energy of N and NHx (x=1,2) groups on (5,5) and (8,0) SiCNTs ranges from -1.82 to -7.19 eV. The electronic structures of SiCNTs can be effectively modified by these groups and display diverse characters ranging from semiconducting to semimetallic, depending on the chirality of SiCNTs as well as the way of the incorporation of these functional groups. The relationship between the electronic structures and the configurations of these functionalized SiCNTs is also addressed by performing projected density of states combined with Milliken population analysis. These results are expected to open a way to tune the electronic structures of SiCNTs which may have promising applications in building nanodevices.

Journal Article↗