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PubMed1998

Ab initio electronic structure calculation of a new gene system using the negative factor counting method.

We report a calculation of the electronic structure (density of states and molecular orbitals) of a new gene system-the plasmid shuttle vector pCRR1-performed at the ab initio Hartree-Fock level. To deal with the aperiodicity of the biopolymer, a vectorized version of a negative factor counting (NFC) program has been implemented. With this efficient tool, DNA molecules of up to 100 deoxynucleotides (approximately 10,000 basis functions at the ab initio level) can be calculated routinely. In our calculation the base sequence of the plasmid is explicitly taken into account and a standard helical structure is assumed. Minimum as well as 6-31G basis sets are used in the calculation, and solvation effects are explicitly included. The calculation shows that solvation does not have a significant effect on the electronic structure of the biopolymer. It is found that the frontier orbitals (HOMO and LUMO) are highly localized on the bases. The interpretation of this result in terms of the frontier molecular orbital theory is that the attack of radiation-induced radicals is mainly on the base moieties.

Models, Genetic↗
PubMed2005

Spin-orbit coupling in O2(upsilon)+O2 collisions: I. Electronic structure calculations on dimer states involving the X 3Sigmag-, a 1Deltag, and b 1Sigmag+ states of O2.

The importance of vibrational-to-electronic (V-E) energy transfer mediated by spin-orbit coupling in the collisional removal of O2(X 3Sigmag-,upsilon>or=26) by O2 has been reported in a recent communication [F. Dayou, J. Campos-Martinez, M. I. Hernandez, and R. Hernandez-Lamoneda, J. Chem. Phys. 120, 10355 (2004)]. The present work provides details on the electronic properties of the dimer (O2)2 relevant to the self-relaxation of O2(X 3Sigmag-,upsilon>>0) where V-E energy transfer involving the O2(a 1Deltag) and O2(b 1Sigmag+) states is incorporated. Two-dimensional electronic structure calculations based on highly correlated ab initio methods have been carried out for the potential-energy and spin-orbit coupling surfaces associated with the ground singlet and two low-lying excited triplet states of the dimer dissociating into O2(X 3Sigmag-)+O2(X 3Sigmag-), O2(a 1Deltag)+O2(X 3Sigmag-), and O2(b 1Sigmag+)+O2(X 3Sigmag-). The resulting interaction potentials for the two excited triplet states display very similar features along the intermolecular separation, whereas differences arise with the ground singlet state for which the spin-exchange interaction produces a shorter equilibrium distance and higher binding energy. The vibrational dependence is qualitatively similar for the three studied interaction potentials. The spin-orbit coupling between the ground and second excited states is already nonzero in the O2+O2 dissociation limit and keeps its asymptotic value up to relatively short intermolecular separations, where the coupling increases for intramolecular distances close to the equilibrium of the isolated diatom. On the other hand, state mixing between the two excited triplet states leads to a noticeable collision-induced spin-orbit coupling between the ground and first excited states. The results are discussed in terms of specific features of the dimer electronic structure (including a simple four-electron model) and compared with existing theoretical and experimental data. This work gives theoretical insight into the origin of electronic energy-transfer mechanisms in O2+O2 collisions.

Journal Article↗
PubMed2001

Dioxygen binding to deoxyhemocyanin: electronic structure and mechanism of the spin-forbidden two-electron reduction of o(2).

Spectroscopically calibrated DFT is used to investigate the reaction coordinate of O(2) binding to Hemocyanin (Hc). A reaction path is calculated in which O(2) approaches the binuclear copper site with increasing metal-ligand overlap, which switches the coordination mode from end-on eta(1)-eta(1), to mu-eta(1):eta(2), then to butterfly, and finally to the planar [Cu(2)(mu-eta(2):eta(2)O(2))] structure. Analysis of the electronic structures during O(2) binding reveals that simultaneous two-electron transfer (ET) takes place. At early stages of O(2) binding the energy difference between the triplet and the singlet state is reduced by charge transfer (CT), which delocalizes the unpaired electrons and thus lowers the exchange stabilization onto the separated copper centers. The electron spins on the copper(II) ions are initially ferromagnetically coupled due to close to orthogonal magnetic orbital pathways through the dioxygen bridging ligand, and a change in the structure of the Cu(2)O(2) core turns on the superexchange coupling between the coppers. This favors the singlet state over the triplet state enabling intersystem crossing. Comparison with mononuclear model complexes indicates that the protein matrix holds the two copper(I) centers in close proximity, which enthalpically and entropically favors O(2) binding due to destabilization of the reduced binuclear site. This also allows regulation of the enthalpy by the change of the Cu--Cu distance in deoxyHc, which provides an explanation for the O(2) binding cooperativity in Hc. These results are compared to our earlier studies of Hemerythrin (Hr) and a common theme emerges where the spin forbiddeness of O(2) binding is overcome through delocalization of unpaired electrons onto the metal centers and the superexchange coupling of the metal centers via a ligand bridge.

Calibration↗
PubMed2002

Electronic structure and reactivity of low-spin Fe(III)-hydroperoxo complexes: comparison to activated bleomycin.

The spectroscopic properties, electronic structure, and reactivity of the low-spin Fe(III)-hydroperoxo complex [Fe(N4Py)(OOH)](2+) (1, N4Py = N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine) are investigated in comparison to those of activated bleomycin (ABLM). Complex 1 is characterized by Raman features at 632 (Fe-O stretch) and 790 cm(-1) (O-O stretch), corresponding to a strong Fe-O bond (force constant 3.62 mdyn/A) and a weak O-O bond (3.05 mdyn/A). The UV-vis spectrum of 1 shows a broad absorption band around 550 nm that is assigned to a charge-transfer transition from the hydroperoxo to a t(2g) d orbital of Fe(III) using resonance Raman and MCD spectroscopies and density functional (DFT) calculations. Compared to low-spin [Fe(TPA)(OH(x))(OO(t)Bu)](x+)(TPA = tris(2-pyridylmethyl)amine, x = 1 or 2), an overall similar Fe-OOR bonding results for low-spin Fe(III)-alkylperoxo and -hydroperoxo species. Correspondingly, both systems show similar reactivities and undergo homolytic cleavage of the O-O bond. From the DFT calculations, this reaction is more endothermic for 1 due to the reduced stabilization of the .OH radical compared to .O(t)Bu and the absence of the hydroxo ligand that helps to stabilize the resulting Fe(IV)=O species. In contrast, ABLM has a somewhat different electronic structure where no pi donor bond between the hydroperoxo ligand and iron(III) is present [Neese, F.; Zaleski, J. M.; Loeb-Zaleski, K.; Solomon, E. I. J. Am. Chem. Soc. 2000, 122, 11703]. Possible reaction pathways for ABLM are discussed in relation to known experimental results.

Antibiotics, Antineoplastic↗
PubMed2005

Changes in electronic structure upon lithium insertion into the A-site deficient perovskite type oxides (Li,La)TiO3.

Investigation on variation of the electronic structure accompanying the electrochemical lithium insertion into the perovskite type oxide, (Li,La)TiO3, has been carried out by X-ray absorption spectroscopy (XAS). During the electrochemical lithium insertion, titanium ion reduced its oxidation state from Ti4+ to Ti3+, while La3+ does not contribute to the reduction reaction resulting from Ti K-edge and La L3-edge XAS, respectively. Furthermore, O K-edge XAS showed marked spectral changes with electrochemical lithium insertion, indicating the electronic structure around oxide ion affected by lithium insertion reaction. From the XAS measurement, we have concluded the variation observed in O K-edge XAS was related to the strong interaction with inserted Li ion. To confirm this, first-principles band calculations were performed for the perovskite structure before and after electrochemical lithium insertion. The calculated results showed that the electron originated from inserted Li transferred to neighboring oxide ion locally as well as to Ti ion. This may be due to local neutralization effect of Li to reduce the electrostatic interaction in the crystal.

Journal Article↗
PubMed1996

Electronic Structure of Bis(2,4-pentanedionato-O,O')oxovanadium(IV). A Photoelectron Spectroscopy, Electronic Spectroscopy, and ab Initio Molecular Orbital Study.

The electronic structure of the title VO(acac)(2) complex has been investigated using effective core potential configuration interaction ab initio calculations, UV-photoelectron spectroscopy, and electronic spectroscopy. The metal-ligand bonding with the equatorial acac(-) ligands is dominated by sigma interactions involving the filled ligand orbitals and the empty orbitals of the d(1) vanadium(IV) ion. The oxovanadium interactions involve a larger metal-d participation thus resulting in a strong V-O bonding having partial triple-bond character. Additional three-orbital-four-electron stabilizing interactions involving the filled acac(-) MOs and the oxovanadium orbitals further reinforce both the axial and equatorial bonds. The unpaired metal-d electron is completely localized in the nonbonding d(x)()()2(-)(y)()()2 orbital. The low ionization energy of the photoelectron spectrum has been fully assigned on the basis of combined DeltaSCF and configuration interaction calculations. The same theoretical approach has, in addition, provided a good fitting of frequencies associated with "d-d" and charge transfer electronic transitions.

Journal Article↗
PubMed2003

Spectroscopic characterization of the Leu513His variant of fungal laccase: effect of increased axial ligand interaction on the geometric and electronic structure of the type 1 Cu site.

A variety of spectroscopic techniques, combined with density functional calculations, are used to describe the electronic structure of the Leu513His variant of the type 1 Cu site in Myceliophthora thermophila laccase. This mutation changes the type 1 Cu from a blue to a green site. Electron paramagnetic resonance (EPR), optical absorption, circular dichroism, and magnetic circular dichroism (MCD) spectroscopies reveal that, relative to the trigonal planar blue type 1 Cu site in wild-type fungal laccase, the covalency and the ligand field strength at the Leu513His green type 1 Cu center decrease. Additionally, there is a significant reorientation of the d(x)()()2(-)(y)()()2( )singly occupied MO, such that the overlap with the Cys sulfur valence orbital changes from pi to sigma. A density functional study in which internal coordinates are systematically altered reveals that these changes are due to the increased strength of the axial ligand (none to His), leading to a tetragonal distortion and elongation of the equatorial Cu-ligand bonds. These calculations provide insight into the experimental differences in the EPR parameters, charge-transfer absorption spectrum, and ligand-field MCD spectrum between the axial-His variant and blue Cu centers (plastocyanin and the type 1 site in fungal laccase). There are also significant differences between the green site in the Leu513His variant and other naturally occurring, green type 1 Cu sites such as in nitrite reductase, which have short axial Cu-S(Met) bonds. The large difference in EPR parameters between these green type 1 sites derives from a change in ligand field excitation energies observed by MCD, which reflects a decrease in ligand field strength. This is associated with different steric interactions of a His vs an axial Met ligand in a tetragonally distorted type 1 site. Changes in the electronic structure of the Cu site correlate with the difference in reactivity of the green His variant relative to blue wild-type fungal laccase.

Amino Acid Substitution↗
PubMed2002

Tuning of electronic structures of quasi-one-dimensional bromo-bridged Ni(III) complexes with strong electron-correlation by doping of Co(III) ions, [Ni(1-x)Co(x)(Chxn)(2)Br]Br(2).

We have succeeded in synthesizing the Ni(III) complexes doped by Co(III) ions, [Ni(1-x)Co(x)(chxn)(2)Br]Br(2) (x = 0, 0.043, 0.093, and 0.118) by using an electrochemical oxidation method. The single-crystal reflectance spectrum of x = 0.118 shows an intense CT band about 0.5 eV, which is lower than that of [Ni(chxn)(2)Br]Br(2) (1.3 eV). The single-crystal electrical conductivities at room temperature of these compounds increase with increase of the amounts of doping of Co(III) ions. In the ESR spectra, peak-to-peak line widths DeltaH(pp) at room temperature change about 600 G in [Ni(chxn)(2)Br]Br(2) to 200 G in x = 0.118. Such a large x dependence of DeltaH(pp) seems to be ascribed to the increasing contribution from the increasing Curie spins which have smaller line width. Therefore, we have tuned the electronic structures of quasi-one-dimensional bromo-bridged Ni(III) complexes with strong electron correlations by doping of Co(III) ions.

Journal Article↗
PubMed2002

Probing the electronic structure of [MoOS(4)](-) centers using anionic photoelectron spectroscopy.

Using photodetachment photoelectron spectroscopy (PES) in the gas phase, we investigated the electronic structure and chemical bonding of six anionic [Mo(V)O](3+) complexes, [MoOX(4)](-) (where X = Cl (1), SPh (2), and SPh-p-Cl (3)), [MoO(edt)(2)](-) (4), [MoO(bdt)(2)](-) (5), and [MoO(bdtCl(2))(2)](-) (6) (where edt = ethane-1,2-dithiolate, bdt = benzene-1,2-dithiolate, and bdtCl(2) = 3,6-dichlorobenzene-1,2-dithiolate). The gas-phase PES data revealed a wealth of new electronic structure information about the [Mo(V)O](3+) complexes. The energy separations between the highest occupied molecular orbital (HOMO) and HOMO-1 were observed to be dependent on the O-Mo-S-C(alpha) dihedral angles and ligand types, being relatively large for the monodentate ligands, 1.32 eV for Cl and 0.78 eV for SPh and SPhCl, compared to those of the bidentate dithiolate complexes, 0.47 eV for edt and 0.44 eV for bdt and bdtCl(2). The threshold PES feature in all six species is shown to have the same origin and is due to detaching the single unpaired electron in the HOMO, mainly of Mo 4d character. This result is consistent with previous theoretical calculations and is verified by comparison with the PES spectra of two d(0) complexes, [VO(bdt)(2)](-) and [VO(bdtCl(2))(2)](-). The observed PES features are interpreted on the basis of theoretical calculations and previous spectroscopic studies in the condensed phase.

Anions↗
PubMed2001

The electronic structure of the flavin cofactor in DNA photolyase.

Density functional theory is used to calculate the electronic structure of the neutral flavin radical, FADH(*), formed in the light-induced electron-transfer reaction of DNA repair in cis,syn-cyclobutane pyrimidine dimer photolyases. Using the hybrid B3LYP functional together with the double-zeta basis set EPR-II, (1)H, (13)C, (15)N, and (17)O isotropic and anisotropic hyperfine couplings are calculated and explained by reference to the electron densities of the highest occupied molecular orbital and of the unpaired spin distribution on the radical. Comparison of calculated and experimental hyperfine couplings obtained from EPR and ENDOR/TRIPLE resonance leads to a refined structure for the FAD cofactor in Escherichia coli DNA photolyase. Hydrogen bonding at N3H, O4, and N5H results in significant changes in the unpaired spin density distribution and hyperfine coupling constants. The calculated electronic structure of FADH(*) provides evidence for a superexchange-mediated electron transfer between the cyclobutane pyrimidine dimer lesion and the 7,8-dimethyl isoalloxazine moiety of the flavin cofactor via the adenine moiety.

Crystallography, X-Ray↗
PubMed2002

X-ray emission spectroscopy of hydrogen bonding and electronic structure of liquid water.

We use x-ray emission spectroscopy to examine the influence of the intermolecular interaction on the local electronic structure of liquid water. By comparing x-ray emission spectra of the water molecule and liquid water, we find a strong involvement of the a(1)-symmetry valence-orbital in the hydrogen bonding. The local electronic structure of water molecules, where one hydrogen bond is broken at the hydrogen site, is separately determined. Our results provide an illustration of the important potential of x-ray emission spectroscopy for elucidating basic features of liquids.

Journal Article↗
PubMed2006

Local electronic structure around a single Kondo impurity.

The local electronic structure due to the adsorption of Co on Cu111 is studied using an embedded cluster model, in which the crystal background is taken into account via an effective density functional theory (DFT)-based potential. This approach goes beyond the usual single-impurity Anderson model, where the ground state consists of a singly occupied impurity whose moment is compensated by the background conduction electrons. Ab initio correlated wave function calculations for the embedded cluster provide an alternative picture for this ground state and indicate that the quenching of the Co magnetic moment is due to the formation of metal-metal bonds with the Cu substrate. Low-lying excitations are also studied within the embedding model, and our results are discussed in the context of scanning tunneling microscopy experiments (Manoharan, H. C.; Lutz, C. P.; Eigler, D. M. Nature 2000, 403, 512), which find a sharp tunneling resonance localized in the vicinity of the Co adatom.

Adsorption↗
PubMed2005

X-ray absorption spectroscopic study on the electronic structure of Li(1)(-)(x)()CoPO(4) electrodes as 4.8 V positive electrodes for rechargeable lithium ion batteries.

Changes in the electronic structure of olivine Li(1-x)CoPO(4), 4.8 V positive electrode material for lithium ion batteries, were investigated using the X-ray absorption spectroscopy (XAS) technique. The threshold energy in the Co K-edge increased with electrochemical Li removal, indicating the oxidation of cobalt ions due to charge compensation. Moreover, P and O K-edge XAS showed a slight shift in threshold energy with Li removal. Although it is generally believed that the electrons of PO(4) polyanion do not contribute to the oxidation process, present experimental results indicate changes in the electronic structure around PO(4) units. Such results would be interpreted by the idea of the hybridization effect between the Co 3d and O 2p orbitals and of the polarization effect introduced by Li ions.

Journal Article↗
PubMed2006

Atomic and electronic structures of carbon nanotubes on Si(001) stepped surfaces.

We report first-principles total-energy calculations that provide energetics and electronic structures of adsorbed carbon nanotubes (CNTs) on stepped Si(001) surfaces. We find that adsorption energies strongly depend on the directions of CNTs, and that there are several metastable adsorption sites both on terraces and near step edges. We also find that the electronic structure of adsorbed metallic CNTs becomes semiconducting or remains metallic, depending on the adsorption site. Charge redistribution upon adsorption is prominent mainly at the CNT-surface interface.

Journal Article↗
PubMed2006

Electronic structure of charge- and spin-controlled Sr(1-(x+y))La(x+y)Ti(1-x)Cr(x)O3.

We present the electronic structure of Sr(1-(x+y))La(x+y)Ti(1-x)Cr(x)O3 investigated by high-resolution photoemission spectroscopy. In the vicinity of the Fermi level, it was found that the electronic structure was composed of a Cr 3d local state with the t(2g)3 configuration and a Ti 3d itinerant state. The energy levels of these Cr and Ti 3d states are well interpreted by the difference of the charge-transfer energy of both ions. The spectral weight of the Cr 3d state is completely proportional to the spin concentration x irrespective of the carrier concentration y, indicating that the spin density can be controlled by x as desired. In contrast, the spectral weight of the Ti 3d state is not proportional to y, depending on the amount of Cr doping.

Journal Article↗
PubMed2006

Chemical control of electronic structure and superconductivity in layered borides and borocarbides: understanding the absence of superconductivity in LixBC.

The synthetic search for materials related to the 39 K superconductor MgB2 has been difficult. The most promising theoretical suggestion, hole doping of LiBC, does not lead to a new superconductor. We show here that a combination of density functional theory (DFT) calculations, materials synthesis, and structural characterization reveals the origin of the puzzling absence of superconductivity in Li1/2BC as a subtle change in the electronic structure driven by structural response to the introduction of holes. This indicates that the unique aspects of the electronic structure of MgB2 will be demanding to replicate in other systems.

Journal Article↗
PubMed2006

Photoelectron spectra and electronic structure of some 4-substituted 2-allylanisoles.

The electronic structures of 4-substituted 2-allyl anisoles (1-9) have been investigated by ultraviolet photoelectron spectroscopy and quantum chemical methods. The ionisation potentials corresponding to the pi MOs pi(2) and pi(3) of the phenyl ring, and the n(O) orbital of the methoxy group as well as the allylic pi(C=C) orbital could be determined and assigned for 1-9. Linear regression analyses of the IPs related to these orbitals with different substituent constants indicated that Hammett sigma(p) values performed satisfactorily to fair for pi(2), pi(3) and n(O) but poor for allylic pi(C=C). Other substituent constants such as R and R(-) were fair only for pi(2) and pi(3), but poor for n(O) and pi(C=C).

Anisoles↗
PubMed2004

Spectroscopic properties and quantum chemistry-based normal coordinate analysis (QCB-NCA) of a dinuclear tantalum complex exhibiting the novel side-on end-on bridging geometry of N2: correlations to electronic structure and reactivity.

The vibrational properties and the electronic structure of the side-on end-on N(2)-bridged Ta complex ([NPN]Ta(micro-H))(2)(micro-eta(1):eta(2)-N(2)) (1) (where [NPN] = (PhNSiMe(2)CH(2))(2)PPh) are analyzed. Vibrational characterization of the Ta(2)(micro-N(2))(micro-H)(2) core is based on resonance Raman and infrared spectroscopies evaluated with a novel quantum chemistry-based normal coordinate analysis (QCB-NCA). The N-N stretching frequency is found at 1165 cm(-)(1) exhibiting a (15)N(2) isotope shift of -37 cm(-)(1). Four other modes of the Ta(2)N(2)H(2) core are observed between 430 and 660 cm(-)(1). Two vibrations of the bridging hydrido ligands are also identified in the spectra. On the basis of experimental frequencies and the QCB-NCA procedure, the N-N force constant is determined to be 2.430 mdyn A(-)(1). The Ta-N force constants are calculated to be 2.517 mdyn A(-)(1) for the Ta-eta(1)-N(2) bond and 1.291 and 0.917 mdyn A(-)(1) for the Ta-eta(2)-N(2) bonds, respectively. DFT calculations on 1 suggest that the bridging dinitrogen ligand carries a charge of -1.1, which is equally distributed over the two nitrogen atoms. However, orbital analysis reveals that the terminal nitrogen makes lower contributions to the pi orbitals and much higher contributions to the pi orbitals of the N(2) ligand than the bridging nitrogen. This suggests that reactions of the dinitrogen ligand with electrophiles should preferentially occur at the terminal N atom, in agreement with experimental results.

Journal Article↗