Overlap Population Research Articles

Paired interacting orbitals (PIO) analysis of electronic structures of copper(I) complexes with hydrotris(pyrazolyl)borate ligands

The influence of the hydrotris(pyrazolyl)borate (tpzb) ligand substituents on the electron delocalization of the copper(I) center with carbon monoxide and triphenylphosphine, i.e. the copper(I) carbonyl complexes, [Cu{HB(3,5- iPr 2pz) 3}(CO)] ( 1), [Cu{HB(3,5-Me 2pz) 3}(CO)] ( 2), [Cu{HB(pz) 3}(CO)] ( 3), [Cu{HB(3-CF 3-5-Mepz) 3}(CO)] ( 4), and the copper(I) triphenylphosphine complexes [Cu{HB(3,5- iPr 2pz) 3}(PPh 3)] ( 5), [Cu{HB(3-CF 3-5-Mepz) 3}(PPh 3)] ( 6), are studied by using paired interacting orbitals (PIO) analysis. Carbon monoxide is a weak σ-donor and strong π-acceptor ligand. The Cu(I)–CO interaction is entirely dominated by π back bonding between the two degenerate π∗ orbitals of carbon monoxide and two t 2 type d orbitals of copper(I) ion. This interaction is clearly expressed by two PIOs, PIO-2 and PIO-3, and the strength of this π-acceptability is estimated by the summation of their overlap populations (ΣOP). On the other hand, triphenylphosphine is a strong σ-donor ligand. The Cu(I)–P interaction is dominated by donation from the P atom to the copper(I) ion and expressed by PIO-1, and the strength of this donative interaction ( σ-donationability) is estimated by the overlap population of PIO-1. These results are consistent with experimental data of the C O stretching frequencies by IR spectroscopy and of 13C chemical shifts of 13C O and the broadness of the 31P signals of PPh 3 by 13C and 31P NMR spectroscopy.

Electronic structure of SiC (310) twin boundary doped with B, N, Al and Ti

Doping of boron, nitrogen, aluminum and titanium in the SiC (310) twin boundary was investigated, and the first-principle calculation was used to analyze the underlying mechanism of excellent creep resistance and strength of Sylramic and Tyranno SA SiC fibers. The electronic structures were also analyzed and compared. The results of Mulliken overlap populations, electron density differences and density of states reveal that doping of B or N atom reinforces SiC GBs bonding, however, doping of Al or Ti atom weakens SiC GBs bonding. The reinforced SiC GBs will largely prevent atoms from sliding near GBs. The experimental results would be one of the reasons which lead to the reinforcement of either creep resistance or the strength of SiC fibers.

Synthesis, crystal structure, electronic structure, bonding, photoluminescence and spectroscopic property investigations of a mononuclear 1,10-phenanthroline and 5-bromo-salicylate ternary indium(III) complex

The synthesis, X-ray structure, electronic structure, bonding, photoluminescence, spectroscopic property and characterization of an indium(III) complex, [In(Hbsac) 3(phen)] ( 1) (H 2bsac = 5-bromo-salicylic acid, and phen = 1,10-phenanthroline) are presented. Complex 1 is octacoordinate and carboxylate chelating, being novel and rarely reported for main group complexes. The electronic structure, bonding and the charge transfer properties of light excitation and light emission are discussed in detail using first-principles theory, including partial density of states (PDOSs), crystal orbital overlap population (COOP), the density functional theory (DFT/TDDFT) analysis schemes. The charge transfer is mainly π → π ∗ intraligand charge transfer transition (ILCT) for excitation, and π → π ∗ ligand-to-ligand charge transfer transition (LL′CT) for emission in nature.

La7Os4C9의 전자구조와 화학결합

고체 화합물 La7Os4C9 속에 있는 [Os4C9]21‑ 사슬의 전자구조와 화학결합을 extended Hückel 계산 결과에 의해서 논의하였다. 탄소 원자는 물론 (C2)2‑ 분자의 결합 특성은 비교적 큰 Os-C 상호작용을 나 타내었고 특히 (C2)2‑ 분자의 결합길이 증가는 Fermi level 바로 아래에 Os-C2(1 πg) 결합 밴드의 존재로 인 해서 반결합 1πg 오비탈에 부분적인 전자점유가 일어나기 때문인 것으로 해석된다. In the recently synthesized rare earth transition metal carbide <TEX>$La_7O_{s4}C_9$</TEX> one finds one-dimensional organometallic <TEX>$[O_{s4}C_9]^{21-}$</TEX> polymers embedded in a <TEX>$La^{3+}$</TEX> ionic matrix. The electronic structure of the polymeric <TEX>$[O_{s4}C_9]^{21-}$</TEX> chain was investigated by density of states (DOS) and crystal orbital overlap population (COOP), using the extended Huckel algorithm. A fragment molecular orbital analysis is used to study the bonding characteristics of the <TEX>$C_2$</TEX> units in <TEX>$La_7O_{s4}C_9$</TEX> containing <TEX>$C_2$</TEX> units and single C atoms as well. The title compound contains partially filled Os and carbon bands leading to metallic conductivity. As the observed distances already indicated, the calculations show extensive Os-C interactions. The C-C bond distance in the diatomic <TEX>$C_2$</TEX> units (<TEX>$d_{C-C}$</TEX>=131 pm) in the solid is significantly increased relative to <TEX>$<TEX>${C_2}^{2-}$</TEX>$</TEX> or acetylene, because antibonding <TEX>$1{\pi}_g$</TEX> orbitals are partially filled by the Os-<TEX>$C_2(1\;{\pi}_g)$</TEX> bonding contribution found at and below the Fermi level.

Quantum chemical calculations for understanding and predicting toxicity. II. The phosphorylation step in the inhibition of ache by organophosphorus anticholinesterases

The first step in the inhibition of acetylcholinesterase (AChE) by organophosphorus anticholinesterases is formation of the organophosphorous molecule-AChE complex. In the first paper of this series it was shown that the first step can be modeled well by the use of three-dimensional electrostatic molecular potential contour maps around the P compound. The second phosphorylation step of the mechanism by which organophosphorous anticholinesterases of the general formula inhibit AChE is related to the acidity of X and to the bond strength of the P—X bond. For a series of compounds, aryl N-methyl methyl phosphoramidates, in which the P—X bond is constant, this paper shows that the quantum chemically calculated P-O total overlap populations (TOPs) correlate the experimental log I50 for inhibition of AChE over four orders of magnitude with correlation coefficients of 0.96 [r2: TOP 0.9581; (TOP)1/2 0.9614].

Ab Initio MODPOT/VRDDO/MERGE calculations on energetic compounds. II. Nitroexplosives: RDX and α-, β- and δ-HMX

Ab initio MODPOT/VRDDO calculations have been carried out on RDX and α-,β-, and δ-HMX using our ab initio programs that incorporate several desirable options for calculations on large molecules. Among these are ab initio effective core model potentials (MODPOT) that permit calculations of valence electrons only explicitly, yet accurately, and a charge-conserving integral prescreening evaluation (which we named VRDDO—variable retention of diatomic differential overlap) that is especially effective for spatially extended molecules. The resultant theoretical indices are relevant to a number of properties and behaviorial characteristics of these molecules, both intra- and intermolecular. The charges on the atoms (from the gross atomic populations) are needed for calculation of the atomic multipole-atomic multipole electrostatic contributions (a major or dominant factor) to the intermolecular interaction energies. These electrostatic interaction energies are part of the input necessary for calculations on crystal packing and densities of these molecules. The total overlap populations between atoms are related to the inherent bond strengths, which are of interest in predicting and tracing initiating steps of explosive phenomena. The molecular orbital energies of the lowest unoccupied orbitals are of particular interest since these nitroexplosives have been implicated in testicular toxicity and the initial metabolic activation appears to proceed through a one-electron reduction of the nitroexplosive.

Theoretical treatment of hydrogen abstraction by hot tritium atoms

Extended Huckel calculations using Cusachs's modification were performed for the methane–tritium system with the objective of determining how the overlap populations (and energies) varied as a function of GHT distances. The model chosen was axial attack of the hot tritium atom along the CH(1) bond direction which leads to abstraction of the H(1) atom. A position of maximum H(1)T overlap population was found at about the same place as the position of minimum CH(1) overlap population, thus setting certain limits on geometric configurations which would be expected to undergo the H(1) abstraction reaction. Attention is drawn to the pertinence of overlap population results to the bond energy–bond order method of Johnston for obtaining potential energy surfaces. The overlap populations also indicate why in compounds containing very electronegative substituents, the abstraction reaction occurs at a lower energy than would be predicted by the simple bond dissociation energy dependence found experimentally by Rowland for all other systems. A potential energy surface was also traced out for the CH4–T reaction and a basin was found indicating a stable CH4T (or CH5) molecule. Examination of activation energies calculated previously by Eyring and Polyani for axial attack compared to direct attack shows clearly why at low kinetic energies of T the abstraction reaction is favored over the substitution reaction; and why only the abstraction reaction occurs at T kinetic energies lower than ∼1.8 eV.

Comparison for pyrrole and pyrazole of orbital energies and population analyses from ab-initio SCF, CNDO/2, INDO, extended hückel, and ARCANA calculations

The results of our recent ab-initio SCF calculations on pyrrole and pyrazole using large Gaussian basis sets are compared to those using less rigorous methods: CNDO/2, INDO, PCILO extended Huckel, and ARCANA (a type of iterative extended Huckel calculation). The ab-initio orbital energies are higher in energy than all those resulting from less rigorous methods. For the two highest occupied orbitals, both of π type, (pyrrole— 1a2 and 2b1; pyrazole—3a″ and 2a″) there was excellent agreement between the measured photoelectron spectroscopic ionization potentials and the Koopman's theorem values from the ab-initio results. Thus the orbital energies calculated by the less rigorous methods all lie too low in energy. The CNDO/2 and INDO orbital energies also span too large a width for the valence band compared to the ab-initio results. The gross atomic populations from the CNDO/2, INDO and PCILO methods show discrepancies from the ab-initio results for both the heteroatoms and the hydrogens. Total overlap populations calculated from the ab-initio SCF wave functions show large negative overlap populations between nonbonded ring atoms. Using the off-diagonal density matrix elements from CNDO/2 and INDO wave functions as if they were true off-diagonal elements from non-ZDO calculations, scaling them (shown previously to lead to reasonable values for TOPS between bonded atoms) led to TOPS between nonbonded ring atoms that were essentially zero. Wiberg bond indices, by definition only capable of giving positive numbers, also cannot reproduce these negative overlap populations. The extended Huckel and ARCANA methods, which are non-ZDO methods, both gave negative tops between nonbonded ring atoms, although not as large as those which resulted from ab-initio calculations.

Molecular calculations with the MODPOT, VRDDO, and MODPOT/VRDDO procedures. V. Ab initio and MODPOT LCAO-MO-SCF calculations on the chlorofluoromethanes

Ab initio LCAO-MO-SCF calculations were carried out on the chlorofluoromethanes CF4, CF3Cl, CF2Cl2, CFCl3, and CCl4 both with a minimum STO 4–3G basis set and with a larger, extended s. p basis set. Ab initio effective core model potential (31G/MODPOT) calculations were then carried out on this same series of chlorofluoromethanes. Valence orbital energies, core orbital energies, total energies, gross atomic populations, total overlap populations, and dipole moments are presented for comparison among the various computational results as well as to measured experimental properties. The results of the 31G/MODPOT calculations compared favorably with those from the ab initio larger extended s. p basis set, which themselves were in better agreement with experiment than those from the ab initio minimum 4–3G set.

Molecular calculations with the MODPOT, VRDDO, and MODPOT/VRDDO procedures: I. HF, F2, HCl, Cl2, formamide, pyrrole, pyridine, and nitrobenzene

The nonempirical valence electron LCAO-MO-SCF model potential (MODPOT) procedure of Bonifacic and Huzinaga has been applied to the HF, F2, HCl, Cl2, formamide, pyrrole, pyridine, and nitrobenzene molecules. The results indicate that the method gives quite accurate valence orbital energies and potential energy curves for diatomics composed of first- and second-row atoms. It gives quite reliable valence orbital energies, gross atomic populations, total overlap populations, and dipole moment for moderately large organic molecules composed of first-row atoms and hydrogen. Use of the MODPOT approximation results in a substantial reduction in computer time and number of two-electron integrals that have to be processed. The nonempirical LCAO-MO-SCF charge-conserving variable retention of diatomic differential overlap (VRDDO) approximation of Wilhite and Euwema has been applied to the pyrrole, pyridine, and nitrobenzene molecules. The results indicate that the procedure gives accurate orbital energies, total energy, gross atomic populations, total overlap populations, and dipole moment for moderately large organic molecules. Use of the VRDDO approximation results in a substantial reduction in computer time. We also present pyrrole, pyridine, and nitrobenzene results obtained by introducing the VRDDO approximation into the MODPOT procedure. The accuracy of the VRDDO method remains unchanged if one considers only the valence electrons and there is an additional reduction in computer time.

BaHg2Tl2. An Unusual Polar Intermetallic Phase with Strong Differentiation between the Neighboring Elements Mercury and Thallium

High yields of the novel BaHg(2)Tl(2) are achieved from reactions of the appropriate cast alloys at approximately 400 degrees C. (Isotypic SrHg(2)Tl(2) also exists.) The tetragonal barium structure (P4(2)/mnm, a = 10.606 A, c = 5.159 A) was refined from both single-crystal X-ray and neutron powder diffraction data in order to ensure the atom site assignments although distances and calculated atom site population also support the results. The Hg and Tl network atoms are distinctive in their functions and bonding. Parallel chains of Hg hexagons and of Tl tetrahedra along c are constructed from polyhedra that share opposed like edges, and these are in turn interconnected by Hg-Tl bonds. Overall, the number of Tl-Tl bonds per cell exceeds the Hg-Hg type by 20:12, but these are approximately 1:2 each in bonding according to their average -ICOHP values (related to overlap populations). Barium is bound within a close 15-atom polyhedron, 12 atoms of which are the more electronegative Hg. LMTO-ASA calculations show that scalar relativistic effects are particularly important for Hg 5d-6s mixing in Hg-Hg and Hg-Tl bonding, whereas relatively separate Tl 6s and 6p states are more important in Tl-Tl interactions. The 6p states of Hg and Tl and 5d of Ba define a dominant conduction band around E(F), and the phase is metallic and Pauli-like paramagnetic. The thallium characteristics here are close to those in numerous alkali-metal-Tl cluster systems. Other active metal-mercury phases that have been studied theoretically are all distinctly electron-richer and more reduced, and without appreciable net 5d, 6s contributions to Hg-Hg bonding.

Hydrogen and carbon interaction in a FeNi alloy with a vacancy

AbstractThe bonding of hydrogen and carbon to Fe and Ni in a 50:50 alloy is analysed using density functional calculations. The changes in the electronic structure of a L10 alloy upon C and H introduction at a vacancy region are addressed and a comparison with H or C in pure metals is drawn. H in bulk FeNi alloy with a vacancy locates at a tetrahedral site shifted towards the vacancy. Instead, C prefers an octahedral site (Fe based). The vacancy acts as strong traps of both C and H. Fe–Ni atoms are initially more strongly bonded to each other due to the vacancy formation. Consequently, the Fe–Fe, Fe–Ni and Ni–Ni bond strengths are diminished as new metal–C or metal–H bonds are formed. The most affected bond is the Fe–Ni, whose overlap population decreases by 72%. An analysis of the orbital interaction reveals that the Fe–H bonding involves mainly the Fe 4s, H 1s and Ni 4s orbitals. In the case of the sequential absorption, the C–H interaction is almost zero at a distance of 2.72 Å. The main interactions of these interstitials are developed with either Fe or Ni. We also consider the absorption sequence (H first or C first) and its influence on the electronic structure. Our results could be relevant to understand some steps of the carburization process during thermal cracking operations where hydrogen atoms are present. (© 2009 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)

Density functional theory study of hexagonal carbon phases

It is reported frequently that the new carbon phases may be harder than diamond (Wanget al 2004 Proc. Natl Acad. Sci. 101 13699 and Mao et al 2003 Science 302 425). However,the mechanism is still unclear. In this paper we systematically investigate the structural,electronic, and mechanical properties of the diamond polytypes using first-principlesdensity functional calculations. The results show that the bulk modulus and shear modulusfor the hexagonal form of diamond approach those of diamond, suggesting they might behard and low compressibility materials. According to the semiempirical method forhardness based on the Mulliken overlap population, the hardnesses for hexagonal formshave been evaluated and compared to diamond. The results indicate that thesephases are superhard. More importantly, the bonds in some specific directions ofthe hexagonal phases are harder than those in diamond, which may lead to thenoticeable indentation marks on the diamond anvils observed in experiments.

Molecular orbital study on a mechanism of adhesion between carbides and optical glass with high refractive index

AbstractA mechanism of adhesion between carbide molds and optical glass species with high refractive index in precision molding was elucidated on the basis of DV‐Xα molecular orbital calculations. An interfacial cluster model comprising NbPNaO glass and glassy carbon (GC) was applied in order to examine the changes in the chemical bonds between atoms at the interface and the effect of the substitution of niobium with other transition metals (denoted with; MdI) at the interface. The bond overlap population (BOP) between oxygen atoms at the surface of the glass and carbon atoms at the surface of the GC increases when the surface of the glass approaches the GC, while that between MeIO correspondingly decreases. When introducing oxygen deficiency at the surface of the glass, the BOP of the MeIcarbon bonds against the MeIoxygen increased in the order of Nb&lt;Ti&lt;W, which mostly coincided with the experimentally obtained order of increased probability of occurrence of adhesion between the glass and the GC mold. This supports the validity of the model where adhesion between the glass and the carbide occurs following the reduction of the transition metal in the glass. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009

Structural, elastic and electronic properties of ACTi 3 (A=Al, In and Tl) antiperovskite

First principle calculations were performed to investigate the structural, elastic and electronic properties of unexplored antiperovskite ACTi 3, with A=Al, In and Tl. The calculated structural parameters were found to be in good agreement with the available experimental data, with deviations being less than 2.7%. The bulk modulus was found to be equal to 155 GPa for AlCTi 3 and to a value 5% lower, 147 GPa, for TlCTi 3. For values of applied pressures up to 40 GPa, elastic moduli were calculated and the mechanical stability criteria were verified. The band structure of these compounds has been found to display a metallic character, with strong ionic–covalent bonds between Ti and C atoms, and ionic bonds along A and Ti atoms. The overlap population analysis showed that the stiffness decreases with an increase in the antibonding state between Ti and A atoms.

Simulation of hydrogen trapping at defects in Pd

Abstract The interaction of hydrogen with defects in palladium was studied using qualitative electronic structure calculations in the framework of the Atom Superposition and Electron Delocalization Molecular Orbital (ASED-MO) theory. Interatomic distances, energies and electronic structure for hydrogen at a dislocation and at a vacancy were determined and compared with that for an octahedral site in the Pd fcc lattice. We found that a repulsive H–H interaction is developed if these atoms occupy interstitial sites in a regular lattice. However, when the H atoms are close to a dislocation, the accumulation becomes possible. It was found that the dislocation allows hydrogen association at interatomic distances close to molecular hydrogen. The Density of States (DOS) and Crystal Orbital Overlap Population (COOP) curves were used to shed more light on the interstitial-Pd-defect interactions. Hydrogen produce changes in the local and global electronic structure of the host metal and induce changes in the cohesive forces between atoms in the host matrix. In all cases, it was found that strong bonds between Pd and H atoms are formed while metal–metal bonds are weakened. The metal–hydrogen bonds were characterized by charge transfer from metal atoms to hydrogen.

티타늄 산화물과 유화물의 전지 전압을 결정하는 요소에 대한 제일원리계산

Electronic structures and chemical bonding of Li-intercalated and were investigated by using discrete variational method as a first-principles molecular-orbital method. structure is the equilibrium structure for , which is widely used as a commercial cathode material for lithium secondary battery. The study especially focused on the charge state of Li ions and the magnitude of covalency around Li ions. The average voltage of lithium intercalation was calculated using pseudopotential method and the average intercalation voltage of was higher than that of . It can be explained by the differences in Mulliken charge of lithium and the bond overlap population between the intercalated Li ions and anions in as well as . The Mulliken charge, which means the ionicity of Li atom, was approximately 0.12 in and the bond overlap population (BOP) indicating the covalency between Ti and S was about 0.339. One the other hands, the Mulliken charge of lithium was about 0.79, which means that Li is fully ionized. The BOP, the covalency between Ti and O, was 0.181 in . Because of high ionicity of Li and the weak covalency between Ti and the nearest anion, has a higher intercalation voltage than that of .

Overlap population diagram for ELNES and XANES: peak assignment and interpretation

This article reviews overlap population (OP) diagrams for electron energy loss near-edgestructure (ELNES) and x-ray absorption near-edge structure (XANES). By using theOP diagrams, peaks in ELNES and XANES of MgO, ZnO, AlN, GaN, InN, andYBa2Cu3O7−x are interpreted in terms of cation–anion and cation–cation interactions. Commonfeatures are found in the OP diagrams for different edges. A reconstruction of theunoccupied electronic structure is demonstrated by aligning the different edges with thecommon features in the OP diagrams. The OP diagram is also applied to theCu/Al2O3 hetero-interface to find the relationships among ELNES, atomic and electronic structures,and properties.

Electronic structure analyses of the interface between a high refractive index optical glass and carbides

High refractive index aspheric glass lenses are often used in digital still cameras. However, in manufacturing, adhesion of softened glass to carbide mold causes various defects on the lens surface. We performed experimental transmission electron microscopy (TEM) observations and molecular dynamics/orbital calculations to investigate the glass–carbide adhesion mechanism. TEM revealed island-shaped glass adhesion on the surface of carbide (glassy carbon: GC). TEM–energy dispersion spectra (EDS) showed reduced atomic ratio of oxygen in adhered glass compared with bulk, indicating adhered glass could undergo reduction. From DV-Xα calculations focused on the oxygen atom on the surface of the glass; OI, as Nb–O I bonds at the glass surface approach GC, an overlap population between O I and C increases while that of the Nb–O I bonds decreases. This suggests that, in agreement with TEM–EDS results, O I of the Nb–O I bond forms no bridging bond such as Nb–O I–C at the glass–GC interface, while the C–O I bonding unit could be isolated at the GC surface, and supports our assumption that reduction of the glass induces adhesion to the GC mold.

In Situ Oxidation of Alkanethiol Groups and Proton Transfer in Nanopores of Sodium Borosilicate Glasses

Porous glasses with 4 nm diameter pores were prepared utilizing a spinodal-type phase separation of Na2O−B2O3−SiO2 glass, and the surface was modified by using mercaptoalkyltrimethoxysilane with different alkyl chain length ((CH3O)3Si(CH2)n-SH, n = 1, 3, 6, 10). The thiol groups (−SH) were oxidized with H2O2 to obtain −SO3H groups. The amount of the introduced silane coupling agents and the reactivity with H2O2 inside the nanopores drastically changed by changing the alkyl chain length (n). The molecular structures, charge distributions, bond overlap populations (BOP) between Si and alkyl chains, as well as net charges of thiol groups were calculated based on a density functional theory and a first-principle theory (DVXα). The charge distribution calculations suggest that oxygen atoms on pores affect significantly for both the net charge of S and BOP, and the BOP values were directly related with the in situ oxidation reactivity of silane coupling agents. The porous glasses modified with the silane coupling agent with n = 1 showed high proton conductivity of 1 × 10−2 S/cm at 80 °C and 90% relative humidity.