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Quantum chemical MNDO study of electronic structure for 29 indazoles has been performed. Statistically significant quantitative relation between some characteristics obtained and radioprotective activity was found out. Indazole structures which data predicted for radioprotective activity (survival, %) are on 50% level or more are proposed.
The electronic structure and spectrum of several models of the binuclear metal site in soluble CuA domains of cytochrome-c oxidase have been calculated by the use of an extended version of the complete neglect of differential overlap/spectroscopic method. The experimental spectra have two strong transitions of nearly equal intensity around 500 nm and a near-IR transition close to 800 nm. The model that best reproduces these features consists of a dimer of two blue (type 1) copper centers, in which each Cu atom replaces the missing imidazole on the other Cu atom. Thus, both Cu atoms have one cysteine sulfur atom and one imidazole nitrogen atom as ligands, and there are no bridging ligands but a direct Cu-Cu bond. According to the calculations, the two strong bands in the visible region originate from exciton coupling of the dipoles of the two copper monomers, and the near-IR band is a charge-transfer transition between the two Cu atoms. The known amino acid sequence has been used to construct a molecular model of the CuA site by the use of a template and energy minimization. In this model, the two ligand cysteine residues are in one turn of an alpha-helix, whereas one ligand histidine is in a loop following this helix and the other one is in a beta-strand.
The changes in the structural and electronic properties accompanying metal ionization of the iron-containing protein, rubredoxin, and of some ligand and metal mutants, have been explored using density functional theory (DFT) calculations of the metal atom coordinated to the four immediate residues. Both isolated and embedded cluster studies have been carried out, the latter using the hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The replacement of a cysteine by a serine residue has a considerable effect on both the electronic and geometric structure of the core, which can be qualitatively understood on the basis of the isolated cluster studies. The modulation of these properties caused by the protein environment is quite accurately described by the QM/MM calculations. The predicted core geometries are in good accord with both X-ray and EXAFS data, and the changes in the redox potentials are predicted, at least semiquantitatively, by considering only the core part of the protein.
The electronic structure and the nature of optical transitions in oxygen dangling bond in silica glass, the nonbridging oxygen hole center (NBOHC), were calculated. The calculation reproduced well the peak positions and oscillator strengths of the well-known optical absorption bands at 2.0 and 4.8 eV, and of the recently discovered absorption band at 6.8 eV. The 2.0 eV band was attributed to transition from the sigma bond between Si and dangling oxygen to nonbonding pi orbital on the dangling oxygen. The uniquely small electron-phonon coupling associated with the 2.0 eV transition is explained by stabilization of Si-O bond in the excited state by hyperconjugation effects.
We report on the results of an exhaustive study of the interplay between the valence electronic structure, the topology and reactivity of orbitals, and the molecular structure of biphenyl by means of Penning ionization electron spectroscopy in the gas phase upon collision with metastable He*(2(3)S) atoms. The measurements are compared with one-particle Green's function calculations of one-electron and shake-up valence ionization spectra employing the third-order algebraic diagrammatic construction scheme [ADC(3)]. Penning ionization intensities are also analyzed by means of the exterior electron-density model and comparison with photoelectron spectra: in contrast with the lines originating from sigma orbitals, ionization lines belonging to the pi-band system have large Penning ionization cross sections due to their greater extent outside the molecular van der Waals surface. The involved chemi-ionization processes are further experimentally investigated using collision-energy-resolved Penning ionization electron spectroscopy. The cross sections of pi-ionization bands exhibit a markedly negative collision-energy dependence and indicate that the interaction potential that prevails between the molecule and the He*(2(3)S) atom is strongly attractive in the pi-orbital region. On the other hand, the partial ionization cross sections pertaining to sigma-ionization channels are characterized by more limited collision-energy dependencies, as a consequence of rather repulsive interactions within the sigma-orbital region. A comparison of ADC(3) simulations with the Penning ionization electron spectra and UV photoelectron spectra measured by Kubota et al. [Chem. Phys. Lett. 1980, 74, 409] on thin films of biphenyl deposited at 170 and 109 K on copper demonstrates that biphenyl molecules lying at the surface of polycrystalline layers adopt predominantly a planar configuration, whereas within an amorphous sample most molecules have twisted structures similar to those prevailing in the gas phase.
The electronic structure of the binuclear copper complex [Cu(2)(L)](3+) [L = N(CH(2)CH(2)N(H)CH(2)CH(2)N(H)CH(2)CH(2))(3)N] has been investigated by resonance Raman and electroabsorption spectroscopy. Crystallographic Cu(2) distances of 2.364(1) and 2.415(1) A determined for the nitrate and acetate salts, respectively, are consistent with a substantial metal-metal interaction. The Cu-Cu bonding interaction in the binuclear complex is modulated both in the solid state and in solution by the ligand environment through coupling to ligand torsional modes that are, in turn, stabilized by hydrogen bonding. Electroabsorption data on the three major visible and near-infrared electronic transitions of Cu(2)L, lambda(max) (epsilon(max)) = 1000 nm ( approximately 1200 M(-1) cm(-1)), 748 nm (5600 M(-1) cm(-1)), and 622 nm (3350 M(-1) cm(-1)), reveal a difference dipole moment between the ground and excited states (Deltamu(A)) because of symmetry breaking. The difference polarizability for all three of the transitions is negative, indicating that the ground state is more polarizable than the excited state. A general model to explain this behavior in terms of the proximity of accessible transitions involving copper d electrons is proposed to explain the larger polarizability of the ground state. Raman excitation profiles (REPs) provide evidence for multiple conformational states of [Cu(2)(L)](3+). Separate REPs were obtained for each of the components of the two major Raman bands for nu(1) (a Cu-Cu stretching mode) and nu(2) (a Cu-Cu-N(eq) bending mode). The Raman data along with quantum chemical ZINDO/S CI calculations provide evidence for isomeric forms of Cu(2)L with strong coupling between the conformation of L and the Cu-Cu bond length.
Electronic structures of hexagonal ice (ice Ih), high-density amorphous ice (HDA), and very high-density amorphous ice (VHDA) are investigated using ab initio density functional theory (DFT) at 77 K under a pressure of 0.1 MPa, focusing on band structure, density of states (DOS), partial density of states (PDOS), and electron density. It is found that the integration intensity of the O-2p bonding band in HDA is 1.53 eV wider than that in the VHDA. Because more 2p electrons in HDA participate the 2p-1s hybridization of O-H. The classical molecular dynamics (MD) method has further been carried out to analyze the hydrogen bond network of HDA and VHDA with larger numbers of water molecules under the same temperature, pressure, and boundary conditions used as those during the DFT calculation. MD results show that there exists some water molecules with five hydrogen bonds in both HDA (4.1 +/- 0.1%) and VHDA (2.8 +/- 0.1%), as compared with the LDA, being consistent with the integration intensity results of PDOS. This result can be used to interpret the physical nature of the similar transition temperature of HDA and VHDA to LDA with different heating rates.
Ab initio electronic structure calculations elucidate the dramatic differences observed in the electronic spectra of the catechol and alizarin molecules upon binding to titanium. Catechol and alizarin are similar chromophores with analogous electronic spectra in the free state. Binding alizarin to titanium red-shifts the spectrum. The binding of catechol to titanium produces a new optically active transition, at the same time preserving the features of the free catechol spectrum. By examining the details of the calculations, we can rationalize the spectral differences in the catechol and alizarin systems by the positioning of the catechol and alizarin pi molecular orbitals relative to the conduction band of TiO(2).
The first use of [Cr(N)Cl4]2- as a starting material in chromium(v) nitrido chemistry is demonstrated in simple, high yield, metathesis reactions with the pseudohalogens SCN- and N3- yielding five-coordinate, labile complexes: [Cr(N)(NCS)4]2- and [Cr(N)(N3)4]2-, which have been crystallized and characterized by single-crystal X-ray diffraction. Reaction of [Cr(N)(NCS)4]2- with 1,10-phenanthroline furnishes six-coordinate [Cr(N)(NCS)3(phen)]- wherein phenanthroline coordinates to the position trans to the nitrido ligand. The trans influence of the nitrido ligand leads to a bond length difference of 0.223 A between the axial and equatorial ligators from the phenanthroline ligand. The absorption band with lowest energy in these pseudo-linear complexes is assigned as the electric dipole forbidden transition d(xy) --> d(x-y) based on intensities and its variation with the nature of the equatorial ligators. This absorption provides the spectrochemical series for the equatorial ligands, which is found to be numerically almost identical to that determined for chromium(III). DFT calculations reproduce the observed structures and corroborate the ligand field picture of the electronic structure of these complexes.
A detailed study of electrochemically deposited molybdenum oxide thin films has been carried out after they were sintered at 250 degrees C. Conductive probe atomic force microscopy (CP-AFM), Raman microscopy, and X-ray photoelectron spectroscopy (XPS) techniques were employed to assess the complex structural, electronic, and compositional properties of these films. Spatially resolved Raman microprobe spectroscopy studies reveal that sintered molybdenum oxide is polymorphous and phase segregated with three types of domains observed comprising orthorhombic alpha-MoO3, monoclinic beta-MoO3, and intermixed alpha-/beta-MoO3. CP-AFM studies conducted in concert with Raman microprobe spectroscopy allowed for correlation between specific compositional regions and localized electronic properties. Single point tunneling spectroscopy studies of chemically distinct regions show semiconducting current-voltage (I-V) behavior with the beta-MoO3 polymorph exhibiting higher electronic conductivity than intermixed alpha-/beta-MoO3 or microcrystalline alpha-MoO3 domains. XPS valence level spectra of beta-MoO3 films display a small structured band near the Fermi level, indicative of an increased concentration of oxygen vacancies. This accounts for the greatly enhanced electronic conductivity of beta-MoO3 as these positively charged cationic defects (anion vacancies) act to trap excess electrons. Connections between structural features, electronic properties, and chemical composition are established and discussed. Importantly, this work highlights the value of using spatially resolved techniques for correlating structural and compositional features with electrochemical behaviors of disordered, mixed-phase lithium insertion oxides.
The theoretical and technical foundations are presented for the efficient relativistic electronic structure theories to treat heavy-atomic molecular systems. This review contains two surveys of four-component and two-component quasi-relativistic approaches. First, we review our highly efficient computational scheme for four-component relativistic ab initio molecular orbital (MO) methods over generally contracted spherical harmonic Gaussian-type spinors (GTSs). Illustrative calculations, which are performed with a new four-component relativistic ab initio molecular orbital program package REL4D, clearly show the efficiency of our computational scheme by the Dirac-Hartree-Fock (DHF) and Dirac-Hartree-Fock (DKS) methods. Next, in the two-component quasi-relativistic framework, two relativistic Hamiltonians, RESC and higher order Douglas-Kroll (DK) Hamiltonians, are introduced, and several illustrative calculations are shown. Numerical results for several systems show that good accuracy can be obtained with our third-order DK (DK3) Hamiltonian.
The valence electronic structures of [Cu(hfac)L] (hfac = CF(3)C(O)CHC(O)CF(3); L = PMe(3), CNMe), [Ag(hfac)(PMe(3))], and [Ag(fod)(PEt(3))] (fod = t-BuC(O)CHC(O)C(3)F(7)) have been studied by recording their photoelectron spectra and by performing Xalpha-SW calculations on the model compounds [M(dfm)(PH(3))] (dfm = HC(O)CHC(O)H; M = Cu, Ag) and [Cu(dfm)(CNH)]. For the copper complexes, the spectra were recorded between 21 and 160 eV using He I, He II and synchrotron radiation; while, for the silver complexes, He I and He II, spectra were recorded. Assignments were made by comparison of experimental and calculated values of band energies, and, for the copper complexes, by similar comparison of experimental and theoretical branching ratios as a function of photon energy. For the silver complexes, a more limited comparison of band intensities in the He I and He II spectra was made. In analogous compounds, it is shown that the binding energies follow the sequence Ag 4d > Cu 3d, with an energy difference of almost 2 eV.
A finite-temperature linear tetrahedron method for electronic structure calculations of periodic systems is developed. When compared to widely used simple temperature broadening, the number of k points necessary for accurate integration at finite temperatures is reduced. The utility of the method is demonstrated with benchmark calculations on 1D, 2D, and 3D systems.
It is shown that standard computations of electronic structures of polyatomic systems that yield the global minimum configuration and vibrational frequencies may be faulty if the symmetry of this configuration is lower than the highest possible one and the origin of this distortion, which is always due to the Jahn-Teller effect, is neglected; this may lead, in particular, to the loss of the Berry phase factor that changes the vibronic energy level spectrum and which we show to be present even when there are no apparent conical intersections. The general case and the ozone molecule are analyzed.
The electronic structure and the unusual EPR parameters of sulfur-centered alkyl thiyl radical from cysteine are investigated by density functional theory (DFT) and correlated ab initio calculations. Three geometry-optimized, staggered conformations of the radical are found that lie within 630 cm(-1) in energy. The EPR g-values are sensitive to the energy difference between the nearly-degenerate singly occupied orbital and one of the lone-pair orbitals (excitation energies of 1732, 1083, and 3429 cm(-1) from Multireference Configuration Interaction calculations for the structures corresponding to the three minima), both of which are almost pure sulfur 3p orbitals. Because of the near degeneracy, the second order correction to the g tensor, which is widely used to analyze g-values of paramagnetic systems, is insufficient to obtain accurate g-values of the cysteine thiyl radical. Instead, an expression for the g tensor must be used in which third order corrections are taken into account. The near-degeneracy can be affected to roughly equal extents by changes in the structure of the radical and by hydrogen bonds to the sulfur. The magnitude of the hyperfine coupling constants for the beta protons of the cysteine thiyl radical is found to depend on the structure of the radical. On the basis of a detailed comparison between experimental and calculated g-values and hyperfine coupling constants an attempt is made to identify the structure of thiyl radicals and the number of hydrogen bonds to the sulfur.
The electronic structure of the whole molecule of acidic phospholipase A2 (PLA2) from the venom of Agkistrodon halys pallas (A. halys pallas) has been calculated using the extended negative factor counting (ENFC) method in which dimers were calculated at the ab initio level using a minimal basis set, with simulation of the aqueous environment. Hopping conductivities were determined by the use of random walk theory. The results show that the frontier orbitals are mainly localized to residues which are involved in the biological activity of acidic PLA2. The C-terminal region might play some important role in biological activity because of its active electrons. The aromatic patch on the surface of the enzyme, together with two neighbouring acidic residues, has very active electrons that may be responsible for the inhibition of platelet aggregation. Trp30, which is involved in the interfacial recognition region, may transfer its electrons to the aggregated substrate. It is also concluded that the conductivity of the protein is caused mainly by holes transported through the valence band rather than electrons transferred in the conductive band. The a.c. conductivity of acidic PLA2 confirms that proteins, if doped, are amorphous conductors. Moreover, the a.c. conductivities of acidic PLA2 are approximately one order of magnitude higher than those of some other proteins. This suggests that the toxicity of acidic PLA2 may be related to its high a.c. conductivity.
We report the geometrical features and electronic structures of di-mu-oxo-bridged Mn-Mn binuclear complexes with H2O ligands [Mn2O2(H2O)8]q+ in the iso- and mixed-valence oxidation states. All of the combinations among Mn(II), Mn(III), and Mn(IV) ions are considered the oxidation states of the Mn-Mn center, and the changes in molecular structure induced by the different electron configurations of Mn-based orbitals are investigated in relation to the oxygen-evolving complex (OEC) of photosystem II. The stable geometries of complexes are determined by using the hybrid-type density functional theory for both of the highest- and lowest-spin couplings between Mn sites, and the lowest-spin-coupled states are energetically more favorable than the highest-spin-coupled states except in the case of the complexes with the Mn(II) ion. The coordination positions of H2O ligands at the Mn(II) site tend to shift from the octahedral positions in contrast to those at the Mn(III) and Mn(IV) sites. The shape of the Mn2O2 core and the distances between the Mn ions and the H2O ligands vary depending on the electron occupations of the octahedral eg orbitals on the Mn site with an antibonding nature for the Mn-ligand interactions, indicating the trend as Mn(II)-O > Mn(III)-O and Mn(IV)-O, O-Mn(II)-O > O-Mn(III)-O > O-Mn(IV)-O among the iso-valence Mn2O2 cores, and O-Mn(lower)-O < O-Mn(higher)-O within the mixed-valence Mn2O2 core, and as Mn(II)-OH2 and Mn(III)-OH2 > Mn(IV)-OH2 for the axial H2O ligand. The optimized geometries of model complexes are compared with the X-ray structure of the OEC, and it is suggested that the cubane-like Mn cluster of the active site may not contain a Mn(II) ion. The effective exchange integrals are estimated by applying the approximate spin projection to clarify the magnetic coupling between Mn sites, and the superexchange pathways through the di-mu-oxo bridge are examined on the basis of the singly occupied magnetic orbitals derived from the singlet-coupled natural orbitals in the broken-symmetry state. The comparisons of the calculated results between [Mn2O2(H2O)8]q+ in this study and [Mn2O2(NH3)8]q+ reported by McGrady et al. suggest that the symmetric pathways are dominant to the exchange coupling constant, and the crossed pathway would be less important for the former than it would for the latter in the Mn(III)-Mn(III), Mn(IV)-Mn(IV), and Mn(III)-Mn(IV) oxidation states.
The spectroscopic and magnetic properties of dioxolene complexes of zinc, copper and nickel were studied by DFT calculations on model complexes of formulas [(NH(3))(4)M(II)(SQ)](+) (M=Zn, Ni; SQ=semiquinonato) and [(NH(3))(2)Cu(II)(SQ)](+). Standard approaches such as time-dependent DFT (TDDFT), the Slater transition state (STS), and broken symmetry (BS) were found to be unable to completely account for the physical properties of the systems, and complete active space-configuration interaction (CAS-CI) calculations based on the Kohn-Sham (KS) orbitals was applied. The CAS-CI energies, properly corrected with multireference perturbation theory (MR-PT), were found to be in good agreement with experimental data. We present here a calculation protocol that has a low CPU cost/accuracy ratio and seems to be very promising for interpreting the properties of strongly correlated electronic systems in complexes of real chemical size.