Chemical bonding variations and electron-phonon interactions

A new functional, Psib(Phi), of an electronic state in solids based on the bonding indicator B(tau,tau') in terms of Mulliken's electron partitioning approach has been introduced. Using Psib(Phi), the bonding variations of an electronic state caused by electron-phonon coupling can be studied. With this proposed approach, the differences between the "flat band" states for Hg in coupling to the phonons and the peaklike structure of electron-phonon coupling constants in the q space are well explained.     

Spectroscopic and electronic structure studies of a dimethyl sulfoxide reductase catalytic intermediate: implications for electron- and atom-transfer reactivity

The electronic structure of a genuine paramagnetic des-oxo Mo(V) catalytic intermediate in the reaction of dimethyl sulfoxide reductase (DMSOR) with (CH(3))(3)NO has been probed by electron paramagnetic resonance (EPR), electronic absorption, and magnetic circular dichroism (MCD) spectroscopies. EPR spectroscopy reveals rhombic g- and A-tensors that indicate a low-symmetry geometry for this intermediate and a singly occupied molecular orbital that is dominantly metal centered. The excited-state spectroscopic data were interpreted in the context of electronic structure calculations, and this has resulted in a full assignment of the observed MCD and electronic absorption bands, a detailed understanding of the metal-ligand bonding scheme, and an evaluation of the Mo(V) coordination geometry and Mo(V)-S(dithiolene) covalency as it pertains to the stability of the intermediate and electron-transfer regeneration. Finally, the relationship between des-oxo Mo(V) and des-oxo Mo(IV) geometric and electronic structures is discussed relative to the reaction coordinate in members of the DMSOR enzyme family.     

INDO/SCF-CI calculations and structural spectroscopic studies of some complexes of 4-hydroxyacetanilide

The electronic energies among different possible structures of 4-hydroxyacetanilide (paracetamol) (PA) molecule, were calculated using INDO method and it has been concluded that its structure has C(s) point group symmetry of the cis-form. The ionization potential, electron affinity, dipole moment and binding energy have been calculated. The calculated electronic transitions of the cis-form of PA using SCF-CI method have good coincidence with the electronic absorption spectrum. The temperature effect on the electronic spectrum of PA confirms the presence of one conformer only. The electronic spectra of PA compound were studied in different polar- and non-polar solvents and the hydrogen bonding as well as the orientation energies of the polar solvents were determined from the mixed solvents studies. Complexes of PA with various metal ions such as, Cu(II), Zn(II) or Fe(II) ions of ratio 2:1, respectively, have been prepared and their structure has been confirmed by elemental analysis, atomic absorption spectra, IR spectra and (1)H NMR spectra and finally it can be concluded that the structure of the complexes has C2h point group symmetry in which two PA molecules are chelated to any one of the metal ions, Cu(II), Zn(II) and Fe(II) ions.     

电场极化对碱基对质子转移和电子传递的影响

在B3LYP/6-31+G**//HF/6-31+G**水平上研究了在不同电场极化环境下碱基对A-T的几何构型和电子结构. 通过碱基对的氢键和结合能的变化讨论了碱基对间的质子转移, 进一步利用密度泛函理论结合非平衡态格林函数方法研究了通过碱基对的电子输运行为. 结果表明, 在0.6～2.0 V的偏压下, 由T向A方向的电子传递更易进行, 表现了微弱的整流行为.     

Probing the structure and bonding in Al6N- and Al6N by photoelectron spectroscopy and ab initio calculations

The electronic and geometrical structure of a nitrogen-doped Al6- cluster (Al6N-) is investigated using photoelectron spectroscopy and ab initio calculations. Photoelectron spectra of Al6N- have been obtained at three photon energies with seven resolved spectral features. The electron affinity of Al6N has been determined to be 2.58 +/- 0.04 eV. Global minimum structure searches for A6N- and its corresponding neutral form are performed using several theoretical methods. Vertical electron detachment energies, calculated using three different methods for the lowest energy structure and a low-lying isomer, are compared with the experimental data. The ground-state structure of Al6N- is established from the joint experimental and theoretical study to consist of an Al2 dimer bonded to the top of a quasi-planar tetracoordinated N unit, Al4N-, or it can be viewed as a distorted trigonal prism structure with the N atom bonded in one of the prism faces. For neutral Al6N, three low-lying isomers are found to compete for the global minimum, two of which are built from the tetracoordinated Al4N unit. The chemical bonding in Al6N- is discussed on the basis of molecular orbital and natural bond analyses.     

负离子光电子能谱技术发展及应用

负离子光电子能谱已经成为探索光谱和化学动力学基础问题的最为重要的技术之一。本文简要介绍了负离子光电子能谱的发展历史,回顾了负离子光电子能谱发展过程中的几种主要技术,包括为了提高分辨率而开发出的零动能能谱和慢电子速度成像技术以及为在气相条件下研究多电荷负离子及其对应中性分子电子特性而开发的电喷雾源与负离子光电子能谱结合的技术。随后介绍其在锕系元素及化合物、含铍化合物的电子结构及成键特征研究中的应用及进展。     

Anomalous behavior of atomic hydrogen interacting with gold clusters

The change in the electronic structure of Au(n)- clusters induced by the exchange of an Au atom by hydrogen is studied using photoelectron spectroscopy. Au anion clusters react with one hydrogen atom but not with molecular hydrogen. The spectra of Au(n)- and Au(n-1)H- clusters show almost identical features for n > 2 suggesting that hydrogen behaves as a protonated species by contributing one electron to the valence pool of the Au(n)- cluster. This behavior is in sharp contrast to that of the commonly understood electronic structure of hydrogen in metals; namely, it attracts an electron from the conduction band of the metal and remains in an "anionic" form or forms covalent bonding. We discuss the influence of the unique electronic structure of H on the unusual catalytic behavior of Au clusters.     

Interplay between size and electronic effects in determining the homogeneity range of the A9Zn4+xPn9 and A9Cd4+xPn9 phases (0 < or = x < or = 0.5), A = Ca, Sr, Yb, Eu; Pn = Sb, Bi

Seven cadmium- and zinc-containing Zintl phases, A9Zn(4+x)Pn9 and A9Cd(4+x)Pn9 (0 < or = x < or = 0.5), A = Ca, Sr, Yb, Eu; Pn = Sb, Bi, have been synthesized, and their structures have been determined by single-crystal X-ray diffraction. All compounds are isostructural and crystallize in the centrosymmetric orthorhombic space group Pbam (no. 55, Z = 2), and their structures feature tetrahedra of the pnicogens, centered by the transition metal. The tetrahedra are not isolated but are connected through corner sharing to form ribbons, which are separated by the divalent cations. The occurrence of a small phase width and its variation across this family of compounds has been systematically studied by variable temperature crystallography, resistivity, and magnetic susceptibility measurements, and these results have been reconciled with electronic structure calculations performed using the tight-binding linear muffin-tin orbital (TB-LMTO-ASA) method. These analyses of the crystal and electronic structure indicate that the polyanionic subnetwork requires 19 additional electrons, whereas only 18 electrons are provided by the cations. Such apparent "electron deficiency" necessitates the presence of an interstitial atom in order for an optimal bonding to be achieved; however, an interplay between the sizes of the cations and anions and the total valence electron concentration (governed by the stoichiometry breadth) is suggested as a possible mechanism for achieving structure stability. The structural relationship between these and some known structures with two-dimensional layers are discussed as well.     

Synthesis, structure, and bonding of BaTl(3): an unusual competition between cluster and classical bonding in the thallium layers.

The new BaTl(3) compound has been synthesized and characterized by physical property measurements and electronic structure calculations. Its structure (Cmcm) is a new intermediate in the Ni(3)Sn family (P6(3)/mmc), and consists of thallium layers formed from two-center bond formation between the parallel chains of face-sharing octahedral clusters. The valence electron concentration (VEC) of the thallium layers is consistent with their two-dimensional nature, in comparison with those in other AX(3)-type compounds with one- or three-dimensional anionic networks with the same building blocks and different VECs. The unique geometric features of the anionic thallium layers bring on an unusual competition between inter- and intracluster bonds. Detailed studies of the energetics of BaTl(3) reveal for the first time the important role of cation-anion interactions in the bonding competition in such an anionic substructure.     

On the nature of metal-carbon bonding: AIM and ELF analyses of MCH(n) (n = 1-3) compounds containing early transition metals

Ab initio and DFT calculations have been performed on a series of organometallic compounds, according to the formula MCH(n), where M = K, Ca, Sc, Ti, V, Cr, or Mn and n = 1-3. Various theoretical methods are compared, the B3LYP level yielding the same agreement with the experimental geometries available as the correlated MP2 and CISD methods, with the 6-311++G(3df,2p) basis set for C and H and Wachter's (15s11p6d3f1g)/[10s7p4d3f1g] basis set for transition metals. The main geometric and electronic features of the molecules studied are described, analyzing the M-C bonding characteristics in terms of the atoms in molecules theory (AIM) and the electron localization function (ELF). Although multiple bonding is expected from the Lewis bonding scheme, the results indicate an almost pure ionic bond for all of the systems studied. The net charge transfer from the metal to the carbon atom ranges from 0.5 to 1 e(-), and the electronic structure of the CH(n)(-) moiety is unaltered after the interaction with the metal cation, showing little or no effect on the shape of the electron pairing. The bond paths corresponding to a possible alpha-agostic bond for these systems are not present.     

The proapoptotic G41S mutation to human cytochrome c alters the heme electronic structure and increases the electron self-exchange rate

The naturally occurring G41S mutation to human (Hs) cytochrome (cyt) c enhances apoptotic activity based upon previous in vitro and in vivo studies, but the molecular mechanism underlying this enhancement remains unknown. Here, X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and density functional theory (DFT) calculations have been used to identify the structural and electronic differences between wild-type (WT) and G41S Hs cyt c. S41 is part of the hydrogen bonding network for propionate 7 of heme pyrrole ring A in the X-ray structure of G41S Hs cyt c and, compared to WT, G41S Hs cyt c has increased spin density on pyrrole ring C and a faster electron self-exchange rate. DFT calculations illustrate an electronic mechanism where structural changes near ring A can result in electronic changes at ring C. Since ring C is part of the solvent-exposed protein surface, we propose that this heme electronic structure change may ultimately be responsible for the enhanced proapoptotic activity of G41S Hs cyt c.     

Electron delocalization and bond formation under the ELF framework

A first approach to the relationship between the electron localization function (ELF) and electronic delocalization upon bond formation is provided. We show from first principles the ability of ELF at the bond critical points to act as an index of the electron reorganization involved in chemical bonding. Simultaneously, this index, that we shall call ELF delocalization index (EDI), constitutes a good measure of electron delocalization. We will show how the core of ELF is proportional to the Wiberg index under the valence bond approach. This relationship will be exploited for some representative examples where EDI is able to identify the stages of bond formation. Furthermore, a maximum in EDI along this process has been found to correlate with the molecular equilibrium configuration, allowing for a formulation of a ??maximal localization principle?? for the stable structure of covalent compounds in terms of ELF.     

The nature of Ru-NO bonds in ruthenium tetraazamacrocycle nitrosyl complexes--a computational study

Ruthenium complexes including nitrosyl or nitrite complexes are particularly interesting because they can not only scavenge but also release nitric oxide in a controlled manner, regulating the NO-level in vivo. The judicious choice of ligands attached to the [RuNO] core has been shown to be a suitable strategy to modulate NO reactivity in these complexes. In order to understand the influence of different equatorial ligands on the electronic structure of the Ru-NO chemical bonding, and thus on the reactivity of the coordinated NO, we propose an investigation of the nature of the Ru-NO chemical bond by means of energy decomposition analysis (EDA), considering tetraamine and tetraazamacrocycles as equatorial ligands, prior to and after the reduction of the {RuNO}(6) moiety by one electron. This investigation provides a deep insight into the Ru-NO bonding situation, which is fundamental in designing new ruthenium nitrosyl complexes with potential biological applications.     

Relativistic effects and gold site distributions: synthesis, structure, and bonding in a polar intermetallic Na6Cd16Au7

Na(6)Cd(16)Au(7) has been synthesized via typical high-temperature reactions, and its structure refined by single crystal X-ray diffraction as cubic, Fm ?3m, a = 13.589(1) ?, Z = 4. The structure consists of Cd(8) tetrahedral star (TS) building blocks that are face capped by six shared gold (Au2) vertexes and further diagonally bridged via Au1 to generate an orthogonal, three-dimensional framework [Cd(8)(Au2)(6/2)(Au1)(4/8)], an ordered ternary derivative of Mn(6)Th(23). Linear muffin-tin-orbital (LMTO)-atomic sphere approximation (ASA) electronic structure calculations indicate that Na(6)Cd(16)Au(7) is metallic and that ～76% of the total crystal orbital Hamilton populations (-ICOHP) originate from polar Cd-Au bonding with 18% more from fewer Cd-Cd contacts. Na(6)Cd(16)Au(7) (45 valence electron count (vec)) is isotypic with the older electron-richer Mg(6)Cu(16)Si(7) (56 vec) in which the atom types are switched and bonding characteristics among the network elements are altered considerably (Si for Au, Cu for Cd, Mg for Na). The earlier and more electronegative element Au now occupies the Si site, in accord with the larger relativistic bonding contributions from polar Cd-Au versus Cu-Si bonds with the neighboring Cd in the former Cu positions. Substantial electronic differences in partial densities-of-states (PDOS) and COHP data for all atoms emphasize these. Strong contributions of nearby Au 5d(10) to bonding states without altering the formal vec are the likely origin of these effects.     

The electronic structure of parallel β-pleated sheets in proteins: An ab initio computation including electron correlation

The electronic structure of a 2D polyglycine network with a pleated sheet structure has been computed at the Hartree–Fock level and by including electron correlation effects within the second order of many-body perturbation theory (electron polaron model). The influence of the size of the atomic basis set and of the extension of the virtual space has been investigated both for single- and many-particle properties. Comparison with the energy of the corresponding single chains showed that interchain interactions (mainly hydrogen bonding) provide an extra stabilization for the 2D network by 7.4 and 10 kcal/mole per glycine residue at the Hartree–Fock and correlated levels, respectively. The energy dispersions are rather anisotropic for all bands whose widths are about 0.5–1 eV along the polypeptide backbones and 0.1–0.2 eV in the perpendicular direction (hydrogen bonds). The HF value of the fundamental energy gap is reduced by 4 eV to 9.2 eV for electron polarons. The wave functions and interaction integrals obtained can be used to calculate further optical and lattice vibrational properties.     

Matrix effects on copper(II)phthalocyanine complexes. A combined continuous wave and pulse EPR and DFT study

The effect of the electron withdrawing or donating character of groups located at the periphery of the phthalocyanine ligand, as well as the influence of polar and nonpolar solvents are of importance for the redox chemistry of metal phthalocyanines. Continuous wave and pulse electron paramagnetic resonance and pulse electron nuclear double resonance spectroscopy at X- and Q-band are applied to investigate the electronic structure of the complexes Cu(II)phthalocyanine (CuPc), copper(II) 2,9,16,23-tetra-tert-butyl-29H,31H-phthalocyanine (CuPc(t)), and copper(II) 1,2,3,4,8,9,10,11,15,16,17,18,22,23,24,25-hexadecafluoro-29H,31H-phthalocyanine (CuPc(F)) in various matrices. Isotope substitutions are used to determine the g values, the copper hyperfine couplings and the hyperfine interactions with the 14N, 1H and 19F nuclei of the macrocycle and the surrounding matrix molecules. Simulations and interpretations of the spectra are shown and discussed, and a qualitative analysis of the data using previous theoretical models is given. Density functional computations facilitate the interpretation of the EPR parameters. The experimental g, copper and nitrogen hyperfine and nuclear quadrupole values are found to be sensitive to changes of the solvent and the structure of the macrocycle. To elucidate the electronic, structural and bonding properties the changes in the g principal values are related to data from UV/Vis spectroscopy and to density functional theory (DFT) computations. The analysis of the EPR data indicates that the in-plane metal-ligand sigma bonding is more covalent for CuPc(t) in toluene than in sulfuric acid. Furthermore, the out-of-plane pi bonding is found to be less covalent in the case of a polar sulfuric acid environment than with nonpolar toluene or H2Pc environment, whereby the covalency of this bonding is increased upon addition of tert-butyl groups. No contribution from in-plane pi bonding is found.     

From aromaticity to self-organized criticality in graphene

The unique properties of graphene are rooted in its peculiar electronic structure where effects of electron delocalization are pivotal. We show that the traditional view of delocalization as formation of a local or global aromatic bonding framework has to be expanded in this case. A modification of the π-electron system of a finite-size graphene substrate results in a scale-invariant response in the relaxation of interatomic distances and reveals self-organized criticality as a mode of delocalized bonding. Graphene is shown to belong to a diverse class of finite-size extended systems with simple local interactions where complexity emerges spontaneously under very general conditions that can be a critical factor controlling observable properties such as chemical activity, electron transport, and spin-polarization.     

UV-vis, IR and 1H NMR spectroscopic studies of some mono- and bis-azo-compounds based on 2,7-dihydroxynaphthalene and aniline derivatives

The absorption spectra of mono- and bis-azo-derivatives obtained by coupling the diazonium salts of aromatic amines and 2,7-dihydroxynaphthalene have been studied in six organic solvents. The different absorption bands have been assigned and the effect of solvents on the charge transfer band is also discussed. The diagnostic IR spectral bands and 1H NMR signals are assigned and discussed in relation to molecular structure. Also, semi-empirical molecular orbital calculations using the atom superposition and electron delocalization molecular orbital (ASED-MO) theory have been performed to investigate the molecular and electronic structures of these compounds. According to these calculations, an intramolecular hydrogen bonding is essential for stabilization of such molecules.     

Electronic structure and bonding of {Fe(PhNO2)}6 complexes: a density functional theory study

Reduction of nitro-aromatic compounds (NACs) proceeds through intermediates with a partial electron transfer into the nitro group from a reducing agent. To estimate the extent of such a transfer and, therefore, the activity of various model ferrous-containing reductants toward NAC degradation, the unrestricted density functional theory (DFT) in the basis of paired L?wdin-Amos-Hall orbitals has been applied to complexes of nitrobenzene (NB) and model Fe(II) hydroxides including cationic [FeOH]+, then neutral Fe(OH)2, and finally anionic [Fe(OH)3]-. Electron transfer is considered to be a process of unpairing electrons (without the change of total spin projection Sz) that reveals itself in a substantial spin contamination of the unrestricted solution. The unrestricted orbitals are transformed into localized paired orbitals to determine the orbital channels for a particular electron-transfer state and the weights of idealized charge-transfer and covalent electron structures. This approach allows insight into the electronic structure and bonding of the {Fe(PhNO2)}6 unit (according to Enemark and Feltham notation) to be gained using model nitrobenzene complexes. The electronic structure of this unit can be expressed in terms of pi-type covalent bonding [Fe+2(d6, S = 2) - PhNO2(S = 0)] or charge-transfer configuration [Fe+3(d5, S = 5/2) - {PhNO2}- ((pi*)1, S = 1/2)].