Importance of interlayer H bonding structure to the stability of layered minerals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Conroy, Michele; Soltis, Jennifer A.; Wittman, Rick S.

Layered (oxy) hydroxide minerals often possess out-of-plane hydrogen atoms that form hydrogen bonding networks which stabilize the layered structure. However, less is known about how the ordering of these bonds affects the structural stability and solubility of these minerals. Here, we report a new strategy that uses the focused electron beam to probe the effect of differences in hydrogen bonding networks on mineral solubility. In this regard, the dissolution behavior of boehmite (γ-AlOOH) and gibbsite (γ-Al(OH)3) were compared and contrasted in real time via liquid cell electron microscopy. Under identical such conditions, 2D-nanosheets of boehmite (γ-AlOOH) exfoliated from the bulkmore » and then rapidly dissolved, whereas gibbsite was stable. Further, substitution of only 1% Fe(III) for Al(III) in the structure of boehmite inhibited delamination and dissolution. Factors such as pH, radiolytic species, and knock on damage were systematically studied and eliminated as proximal causes for boehmite dissolution. Instead, the creation of electron/hole pairs was considered to be the mechanism that drove dissolution. The widely disparate behaviors of boehmite, gibbsite, and Fe-doped boehmite are discussed in the context of differences in the OH bond strengths, hydrogen bonding networks, and the presence or absence of electron/hole recombination centers.« less

Importance of interlayer H bonding structure to the stability of layered minerals

DOE PAGES

Conroy, Michele; Soltis, Jennifer A.; Wittman, Rick S.; ...

2017-10-16

Layered (oxy) hydroxide minerals often possess out-of-plane hydrogen atoms that form hydrogen bonding networks which stabilize the layered structure. However, less is known about how the ordering of these bonds affects the structural stability and solubility of these minerals. Here, we report a new strategy that uses the focused electron beam to probe the effect of differences in hydrogen bonding networks on mineral solubility. In this regard, the dissolution behavior of boehmite (γ-AlOOH) and gibbsite (γ-Al(OH)3) were compared and contrasted in real time via liquid cell electron microscopy. Under identical such conditions, 2D-nanosheets of boehmite (γ-AlOOH) exfoliated from the bulkmore » and then rapidly dissolved, whereas gibbsite was stable. Further, substitution of only 1% Fe(III) for Al(III) in the structure of boehmite inhibited delamination and dissolution. Factors such as pH, radiolytic species, and knock on damage were systematically studied and eliminated as proximal causes for boehmite dissolution. Instead, the creation of electron/hole pairs was considered to be the mechanism that drove dissolution. The widely disparate behaviors of boehmite, gibbsite, and Fe-doped boehmite are discussed in the context of differences in the OH bond strengths, hydrogen bonding networks, and the presence or absence of electron/hole recombination centers.« less

Sub-nanometer surface chemistry and orbital hybridization in lanthanum-doped ceria nano-catalysts revealed by 3D electron microscopy.

PubMed

Collins, Sean M; Fernandez-Garcia, Susana; Calvino, José J; Midgley, Paul A

2017-07-14

Surface chemical composition, electronic structure, and bonding characteristics determine catalytic activity but are not resolved for individual catalyst particles by conventional spectroscopy. In particular, the nano-scale three-dimensional distribution of aliovalent lanthanide dopants in ceria catalysts and their effect on the surface electronic structure remains unclear. Here, we reveal the surface segregation of dopant cations and oxygen vacancies and observe bonding changes in lanthanum-doped ceria catalyst particle aggregates with sub-nanometer precision using a new model-based spectroscopic tomography approach. These findings refine our understanding of the spatially varying electronic structure and bonding in ceria-based nanoparticle aggregates with aliovalent cation concentrations and identify new strategies for advancing high efficiency doped ceria nano-catalysts.

First-Principles Study of the Electronic Structure and Bonding Properties of X8C46 and X8B6C40 (X: Li, Na, Mg, Ca) Carbon Clathrates

NASA Astrophysics Data System (ADS)

KoleŻyński, Andrzej; Szczypka, Wojciech

2016-03-01

Results from theoretical analysis of the crystal structure, electronic structure, and bonding properties of C46 and B6C40 carbon clathrates doped with selected alkali and alkaline earth metals cations (Li, Na, Mg, Ca) are presented. The ab initio calculations were performed by means of the WIEN2k package (full potential linearized augmented plane wave method (FP-LAPW) within density functional theory (DFT)) with PBESol and modified Becke-Johnson exchange-correlation potentials used in geometry optimization and electronic structure calculations, respectively. The bonding properties were analyzed by applying Bader's quantum theory of atoms in molecules formalism to the topological properties of total electron density obtained from ab initio calculations. Analysis of the results obtained (i.a. equilibrium geometry, equation of state, cohesive energy, band structure, density of states—both total and projected on to particular atoms, and topological properties of bond critical points and net charges of topological atoms) is presented in detail.

On the nature of bonding in binary Be2O2 and Si2O2 clusters: rhombic four-center four-electron π and σ bonds.

PubMed

Wang, Kang; Wang, Ying-Jin; Li, Da-Zhi; Ou, Ting; Zhao, Xiao-Yun; Zhai, Hua-Jin

2016-04-14

The structural and electronic properties and chemical bonding of binary Be2O2 and Si2O2 clusters have been studied using quantum chemical calculations at the B3LYP level. For the Be2O2 cluster, the potential energy surface is probed by unbiased structural searches and the global-minimum structure was established using the B3LYP calculations, complemented by PBE0 and single-point CCSD(T) calculations for top isomers. The perfectly planar D2h Be2O2 ((1)Ag) global minimum is well defined, being at least 3.64 eV lower in energy than alternative structures at the CCSD(T)//B3LYP/aug-cc-pVTZ level. Chemical bonding analyses show that D2h Be2O2 and Si2O2 clusters possess the rhombic four-center four-electron (4c-4e) π bond, that is, the o-bond, a conception derived from electron-deficient boron oxide clusters lately. Furthermore, the Be2O2 and Si2O2 clusters also exhibit rhombic 4c-4e σ bonds, both for the radial and tangential σ frameworks (σr and σt). The σt framework is classified as an o-bond only formally, due to the secondary contribution from the Be/Si s component. The three-fold (π, σr, and σt) o-bonds in Be2O2 and Si2O2 are considered to resemble the three-fold aromaticity in all-metal Al4(2-) dianions. A 4c-4e o-bond makes use of four O 2p electrons, which would otherwise be two lone-pairs, for a delocalized and completely bonding orbital, as well as a residual nonbonding orbital. Three-fold o-bonds thus greatly stabilize the binary Be2O2 and Si2O2 clusters. We anticipate that the bonding concept should be applicable to additional molecular systems, including those with larger heterocyclic rings.

Precession technique and electron diffractometry as new tools for crystal structure analysis and chemical bonding determination.

PubMed

Avilov, A; Kuligin, K; Nicolopoulos, S; Nickolskiy, M; Boulahya, K; Portillo, J; Lepeshov, G; Sobolev, B; Collette, J P; Martin, N; Robins, A C; Fischione, P

2007-01-01

We have developed a new fast electron diffractometer working with high dynamic range and linearity for crystal structure determinations. Electron diffraction (ED) patterns can be scanned serially in front of a Faraday cage detector; the total measurement time for several hundred ED reflections can be tens of seconds having high statistical accuracy for all measured intensities (1-2%). This new tool can be installed to any type of TEM without any column modification and is linked to a specially developed electron beam precession "Spinning Star" system. Precession of the electron beam (Vincent-Midgley technique) reduces dynamical effects allowing also use of accurate intensities for crystal structure analysis. We describe the technical characteristics of this new tool together with the first experimental results. Accurate measurement of electron diffraction intensities by electron diffractometer opens new possibilities not only for revealing unknown structures, but also for electrostatic potential determination and chemical bonding investigation. As an example, we present detailed atomic bonding information of CaF(2) as revealed for the first time by precise electron diffractometry.

Molecular and electronic structures of M 2O 7 (M = Mn, Tc, Re)

DOE PAGES

Lawler, Keith V.; Childs, Bradley C.; Mast, Daniel S.; ...

2017-02-21

The molecular and electronic structures for the Group 7b heptoxides were investigated by computational methods as both isolated molecules and in the solid-state. The metal-oxygen-metal bending angle of the single molecule increased with increasing atomic number, with Re 2O 7 preferring a linear structure. Natural bond orbital and localized orbital bonding analyses indicate that there is a three-center covalent bond between the metal atoms and the bridging oxygen, and the increasing ionic character of the bonds favors larger bond angles. The calculations accurately reproduce the experimental crystal structures within a few percent. Analysis of the band structures and density ofmore » states shows similar bonding for all of the solid-state heptoxides, including the presence of the three-center covalent bond. DFT+U simulations show that PBE-D3 underpredicts the band gap by ~0.2 eV due to an under-correlation of the metal d conducting states. As a result, homologue and compression studies show that Re 2O 7 adopts a polymeric structure because the Re-oxide tetrahedra are easily distorted by packing stresses to form additional three-center covalent bonds.« less

The electronic structure of d{sup 6} metal-acetylides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Renshaw, S.K.; Uplinger, A.B.; Bullock, R.M.

1997-12-31

Gas-phase ultraviolet photoelectron spectroscopy has been used to investigate the electronic structure and bonding interactions of d{sup 6} piano-stool metal-acetylides of the general formulas CpML{sub 2}C{triple_bond} C-R [M = Ru, L = PMe{sub 3}, R = H, Me, {sup t}Bu, C{sub 6}H{sub 5}] and CpML{sub 2}C{triple_bond}C-p-C{sub 6}H{sub 4}-NO{sub 2} [M = Fe, Ru, L = CO; M = Ru, L = PMe{sub 3}]. Previous studies of analogous CpFe(CO){sub 2}C{triple_bond}C-R complexes found that the filled-filled interaction between the metal d electrons and the acetylide {pi} bond electrons dominates the shift of the first valence ionizations, and that backbonding of the metalmore » d electrons into the acetylide {pi}* orbitals is very small. It is found here that the change to the second row transition metal and the substitution of phosphines for the carbonyls makes the metal more electron rich, but does not change the basic description of the metal interaction with the acetylide.« less

Substrate Effects for Atomic Chain Electronics

NASA Technical Reports Server (NTRS)

Yamada, Toshishige; Saini, Subhash (Technical Monitor)

1998-01-01

A substrate for future atomic chain electronics, where adatoms are placed at designated positions and form atomically precise device components, is studied theoretically. The substrate has to serve as a two-dimensional template for adatom mounting with a reasonable confinement barrier and also provide electronic isolation, preventing unwanted coupling between independent adatom structures. For excellent structural stability, we demand chemical bonding between the adatoms and substrate atoms, but then good electronic isolation may not be guaranteed. Conditions are clarified for good isolation. Because of the chemical bonding, fundamental adatom properties are strongly influenced: a chain with group IV adatoms having two chemical bonds, or a chain with group III adatoms having one chemical bond is semiconducting. Charge transfer from or to the substrate atoms brings about unintentional doping, and the electronic properties have to be considered for the entire combination of the adatom and substrate systems even if the adatom modes are well localized at the surface.

Amorphous Carbon-Boron Nitride Nanotube Hybrids

NASA Technical Reports Server (NTRS)

Kim, Jae Woo (Inventor); Siochi, Emilie J. (Inventor); Wise, Kristopher E. (Inventor); Lin, Yi (Inventor); Connell, John (Inventor)

2016-01-01

A method for joining or repairing boron nitride nanotubes (BNNTs). In joining BNNTs, the nanotube structure is modified with amorphous carbon deposited by controlled electron beam irradiation to form well bonded hybrid a-C/BNNT structures. In repairing BNNTs, the damaged site of the nanotube structure is modified with amorphous carbon deposited by controlled electron beam irradiation to form well bonded hybrid a-C/BNNT structures at the damage site.

Super-reduced polyoxometalates: excellent molecular cluster battery components and semipermeable molecular capacitors.

PubMed

Nishimoto, Yoshio; Yokogawa, Daisuke; Yoshikawa, Hirofumi; Awaga, Kunio; Irle, Stephan

2014-06-25

Theoretical investigations are presented on the molecular and electronic structure changes that occur as α-Keggin-type polyoxometalate (POM(3-)) clusters [PM12O40](3-) (M = Mo, W) are converted toward their super-reduced POM(27-) state during the discharging process in lithium-based molecular cluster batteries. Density functional theory was employed in geometry optimization, and first-principles molecular dynamics simulations were used to explore local minima on the potential energy surface of neutral POM clusters adorned with randomly placed Li atoms as electron donors around the cluster surface. On the basis of structural, electron density, and molecular orbital studies, we present evidence that the super-reduction is accompanied by metal-metal bond formation, beginning from the 12th to 14th excess electron transferred to the cluster. Afterward, the number of metal-metal bonds increases nearly linearly with the number of additionally transferred excess electrons. In α-Keggin-type POMs, metal triangles are a prominently emerging structural feature. The origin of the metal triangle formation during super-reduction stems from the formation of characteristic three-center two-electron bonds in triangular metal atom sites, created under preservation of the POM skeleton via "squeezing out" of oxygen atoms bridging two metal atoms when the underlying metal atoms form covalent bonds. The driving force for this unusual geometrical and electronic structure change is a local Jahn-Teller distortion at individual transition-metal octahedral sites, where the triply degenerate t2 d orbitals become partially filled during reduction and gain energy by distortion of the octahedron in such a way that metal-metal bonds are formed. The bonding orbitals show strong contributions from mixing with metal-oxygen antibonding orbitals, thereby "shuffling away" excess electrons from the cluster center to the outside of the cage. The high density of negatively charged yet largely separated oxygen atoms on the surface of the super-reduced POM(27-) polyanion allows the huge Coulombic repulsion due to the presence of the excess electrons to be counterbalanced by the presence of Li countercations, which partially penetrate into the outer oxygen shell. This "semiporous molecular capacitor" structure is likely the reason for the effective electron uptake in POMs.

Electron-density descriptors as predictors in quantitative structure--activity/property relationships and drug design.

PubMed

Matta, Chérif F; Arabi, Alya A

2011-06-01

The use of electron density-based molecular descriptors in drug research, particularly in quantitative structure--activity relationships/quantitative structure--property relationships studies, is reviewed. The exposition starts by a discussion of molecular similarity and transferability in terms of the underlying electron density, which leads to a qualitative introduction to the quantum theory of atoms in molecules (QTAIM). The starting point of QTAIM is the topological analysis of the molecular electron-density distributions to extract atomic and bond properties that characterize every atom and bond in the molecule. These atomic and bond properties have considerable potential as bases for the construction of robust quantitative structure--activity/property relationships models as shown by selected examples in this review. QTAIM is applicable to the electron density calculated from quantum-chemical calculations and/or that obtained from ultra-high resolution x-ray diffraction experiments followed by nonspherical refinement. Atomic and bond properties are introduced followed by examples of application of each of these two families of descriptors. The review ends with a study whereby the molecular electrostatic potential, uniquely determined by the density, is used in conjunction with atomic properties to elucidate the reasons for the biological similarity of bioisosteres.

Artificial photosynthetic systems: assemblies of slipped cofacial porphyrins and phthalocyanines showing strong electronic coupling.

PubMed

Satake, Akiharu; Kobuke, Yoshiaki

2007-06-07

This paper reviews selected types of structurally well defined assemblies of porphyrins and phthalocyanines with strong electronic coupling. Face-to-face, head-to-tail, slipped cofacial, and non-parallel dimeric motifs constructed by covalent and non-covalent bonds are compared in the earlier sections. Their molecular orientation, electronic overlap, and absorption and fluorescence properties are discussed with a view towards the development of artificial photosynthetic systems and molecular electronics. Complementary coordination dimers are fully satisfactory in terms of structural stability, orientation factor, pi-electronic overlap, and zero fluorescence quenching. In later sections, several polymeric and macrocyclic porphyrin assemblies constructed by a combination of covalent bonds and complementary coordination bonds are discussed from the viewpoint of light-harvesting antenna functions.

Symmetry and novelty in the electronic and geometric structure of nanoalloys:. the case of Ag27Cu7

NASA Astrophysics Data System (ADS)

Ortigoza, M. Alcántara; Rahman, T. S.

2008-04-01

Nanoparticles of bimetallic alloys have been shown to possess composition dependent characteristics which distinguish themselves from the corresponding bulk alloys. Taking the 34-atom nanoalloy of Ag and Cu (Ag27Cu7), we show using first principles electronic structure calculations that this core-shell alloy indeed has perfect D5h symmetry and consists of only 6 non-equivalent (2 Cu and 4 Ag) atoms. Analysis of the interatomic bond lengths and detailed electronic structure further reveal that the Cu atoms play a major role in controlling the characteristics of the nanoalloy. The higher cohesive energy, together with shorter bond length for Cu, compared to Ag, conspire to produce a hierarchy in the relative strengths of the Ag - Cu, Ag - Ag, and Cu - Cu bonds and corresponding interatomic bond lengths, point to the uniqueness in the characteristics of this nanoalloy. Charge density plots of Ag27Cu7 provide further insights into the relative strengths of the various interatomic bonds.

Electronic shell structure in Ga12 icosahedra and the relation to the bulk forms of gallium.

PubMed

Schebarchov, D; Gaston, N

2012-07-28

The electronic structure of known cluster compounds with a cage-like icosahedral Ga(12) centre is studied by first-principles theoretical methods, based on density functional theory. We consider these hollow metalloid nanostructures in the context of the polymorphism of the bulk, and identify a close relation to the α phase of gallium. This previously unrecognised connection is established using the electron localisation function, which reveals the ubiquitous presence of radially-pointing covalent bonds around the Ga(12) centre--analogous to the covalent bonds between buckled deltahedral planes in α-Ga. Furthermore, we find prominent superatom shell structure in these clusters, despite their hollow icosahedral motif and the presence of covalent bonds. The exact nature of the electronic shell structure is contrasted with simple electron shell models based on jellium, and we demonstrate how the interplay between gallium dimerisation, ligand- and crystal-field effects can alter the splitting of the partially filled 1F shell. Finally, in the unique compound where the Ga(12) centre is bridged by six phosphorus ligands, the electronic structure most closely resembles that of δ-Ga and there are no well-defined superatom orbitals. The results of this comprehensive study bring new insights into the nature of chemical bonding in metalloid gallium compounds and the relation to bulk gallium metal, and they may also guide the development of more general models for ligand-protected clusters.

Shift of semimetal-semiconductor bond direction on “0 1 1” to “1 1 1” Bismuth quazi-two-dimension system

NASA Astrophysics Data System (ADS)

Yazdani, Ahmad; Hamreh, Sajad

2018-03-01

The electronic structure of the nanocrystallines and quasi-two-dimensional systems strongly impressed by the thermodynamic- behavior mainly due to excess of hidden surface free energy. Therefore, the stability of crystalline structure’s change could be related to band-offset of bond rupturing of atomic displacements. whereas for the electronic-structure of "Bi" it seams the competition of L.S and bond exchange should be effectively dominated. Besides all of the characters behave spatial like strong sensitive oxidation here it is supposed that strong correlated electronic structure in the absence of oxygen is resulted on direction of redistribution of surface chemical bond formation before any reconstructive structure. Where • The metallic direction of electronic structure “0 1 1” is changed to “1 1 1” semiconductor direction. • the effect of L.S is more evident on the local density of state while it is not observable around the fermi level. • Strong effect of spin-orbit interaction on splitting of the valance to nearly conduction band around the fermi level is more evident.

Structural changes induced by lattice-electron interactions: SiO2 stishovite and FeTiO3 ilmenite.

PubMed

Yamanaka, Takamitsu

2005-09-01

The bright source and highly collimated beam of synchrotron radiation offers many advantages for single-crystal structure analysis under non-ambient conditions. The structure changes induced by the lattice-electron interaction under high pressure have been investigated using a diamond anvil pressure cell. The pressure dependence of electron density distributions around atoms is elucidated by a single-crystal diffraction study using deformation electron density analysis and the maximum entropy method. In order to understand the bonding electrons under pressure, diffraction intensity measurements of FeTiO3 ilmenite and gamma-SiO2 stishovite single crystals at high pressures were made using synchrotron radiation. Both diffraction studies describe the electron density distribution including bonding electrons and provide the effective charge of the cations. In both cases the valence electrons are more localized around the cations with increasing pressure. This is consistent with molecular orbital calculations, proving that the bonding electron density becomes smaller with pressure. The thermal displacement parameters of both samples are reduced with increasing pressure.

Definition of molecular structure: by choice or by appeal to observation?

PubMed

Bader, Richard F W

2010-07-22

There are two schools of thought in chemistry: one derived from the valence bond and molecular orbital models of bonding, the other appealing directly to the measurable electron density and the quantum mechanical theorems that determine its behavior, an approach embodied in the quantum theory of atoms in molecules, QTAIM. No one questions the validity of the former approach, and indeed molecular orbital models and QTAIM play complementary roles, the models finding expression in the principles of physics. However, some orbital proponents step beyond the models to impose their personal stamp on their use in interpretive chemistry, by denying the possible existence of a physical basis for the concepts of chemistry. This places them at odds with QTAIM, whose very existence stems from the discovery in the observable topology of the electron density, the definitions of atoms, of the bonding between atoms and hence of molecular structure. Relating these concepts to the electron density provides the necessary link for their ultimate quantum definition. This paper explores in depth the possible causes of the difficulties some have in accepting the quantum basis of structure beginning with the arguments associated with the acceptance of a "bond path" as a criterion for bonding. This identification is based on the finding that all classical structures may be mapped onto molecular graphs consisting of bond paths linking neighboring atoms, a mapping that has no known exceptions and one that is further bolstered by the finding that there are no examples of "missing bond paths". Difficulties arise when the quantum concept is applied to systems that are not amenable to the classical models of bonding. Thus one is faced with the recurring dilemma of science, of having to escape the constraints of a model that requires a change in the existing paradigm, a process that has been in operation since the discovery of new and novel structures necessitated the extension of the Lewis model and the octet rule. The paper reviews all facets of bonding beginning with the work of Pauling and Slater in their accounting for crystal structures, taking note of Pauling's advocating possible bonding between large anions. Many examples of nonbonded or van der Waals interactions are considered from both points of view. The final section deals with the consequences of the realization that bonded quantum atoms that share an interatomic surface do not "overlap". The time has come for entering students of chemistry to be taught that the electron density can be seen, touched, and measured and that the chemical structures they learn are in fact the tracings of "bonds" onto lines of maximum density that link bonded nuclei. Matter, as we perceive it, is bound by the electrostatic force of attraction between the nuclei and the electron density.

Bond deformation paths and electronic instabilities of ultraincompressible transition metal diborides: Case study of OsB2 and IrB2

NASA Astrophysics Data System (ADS)

Zhang, R. F.; Legut, D.; Wen, X. D.; Veprek, S.; Rajan, K.; Lookman, T.; Mao, H. K.; Zhao, Y. S.

2014-09-01

The energetically most stable orthorhombic structure of OsB2 and IrB2 is dynamically stable for OsB2 but unstable for IrB2. Both diborides have substantially lower shear strength in their easy slip systems than their metal counterparts. This is attributed to an easy sliding facilitated by out-of-plane weakening of metallic Os-Os bonds in OsB2 and by an in-plane bond splitting instability in IrB2. A much higher shear resistance of Os-B and B-B bonds than Os-Os ones is found, suggesting that the strengthened Os-B and B-B bonds are responsible for hardness enhancement in OsB2. In contrast, an in-plane electronic instability in IrB2 limits its strength. The electronic structure of deformed diborides suggests that the electronic instabilities of 5d orbitals are their origin of different bond deformation paths. Neither IrB2 nor OsB2 can be intrinsically superhard.

Effect of electronic structure of the diamond surface on the strength of the diamond-metal interface

NASA Technical Reports Server (NTRS)

Pepper, S. V.

1981-01-01

A diamond surface undergoes a transformation in its electronic structure by a vacuum anneal at approximately 900 C. The polished surface has no electronic states in the band gap, whereas the annealed surface has both occupied and unoccupied states in the and gap and exhibits some electrical conductivity. The effect of this transformation on the strength of the diamond metal interface was investigated by measuring the static friction force of an atomically clean meta sphere on a diamond flat in ultrahigh vacuum. It was found that low friction (weak bonding) is associated with the diamond surface devoid of gap states whereas high friction (strong bonding) is associated with the diamond surface with gap states. Exposure of the annealed surface to excited hydrogen also leads to weak bonding. The interfacial bond is discussed in terms of interaction of the metal conduction band electrons with the band gap states on the diamond surface. Effects of surface electrical conductivity on the interfacial bond are also be considered.

Density Functionals of Chemical Bonding

PubMed Central

Putz, Mihai V.

2008-01-01

The behavior of electrons in general many-electronic systems throughout the density functionals of energy is reviewed. The basic physico-chemical concepts of density functional theory are employed to highlight the energy role in chemical structure while its extended influence in electronic localization function helps in chemical bonding understanding. In this context the energy functionals accompanied by electronic localization functions may provide a comprehensive description of the global-local levels electronic structures in general and of chemical bonds in special. Becke-Edgecombe and author’s Markovian electronic localization functions are discussed at atomic, molecular and solid state levels. Then, the analytical survey of the main workable kinetic, exchange, and correlation density functionals within local and gradient density approximations is undertaken. The hierarchy of various energy functionals is formulated by employing both the parabolic and statistical correlation degree of them with the electronegativity and chemical hardness indices by means of quantitative structure-property relationship (QSPR) analysis for basic atomic and molecular systems. PMID:19325846

Novel 3D metallic boron nitride containing only sp2 bonds

NASA Astrophysics Data System (ADS)

Wang, Hao; Zhang, Wei; Huai, Ping

2017-09-01

As the closest isoelectronic analogue of carbon, boron nitride (BN) shares a similar structure with carbon from 1D nanotubes, 2D nanosheets, and 3D diamond structures. However, most BN structures are insulators, which limits their application. In this work, under the inspiration of the sp2 hybridized carbon honeycomb, we propose a hexagonal phase of BN consisting of only sp2 bonds, which exhibits intriguingly intrinsic metallicity. First-principles calculations confirm that this phase is both thermally and dynamically stable. Moreover, the calculations on the band structure, partial density states and electron localization function suggest that the metallic behavior is attributable to the delocalized B-2p electrons, leading to second-neighbor interaction between the p z states of sp2-bonded B atoms in adjacent layers. Our findings not only enrich the BN allotrope family with 3D structures but also stimulate further experimental interest in applications of metallic BN in electronic devices.

Electronic structure studies of Ni( 1 0 0 ) surface reconstructions resulting from carbon, nitrogen, or oxygen atom adsorption

NASA Astrophysics Data System (ADS)

Kirsch, Janet E.; Harris, Suzanne

2003-01-01

Solid-state Fenske-Hall band structure calculations have been used to study the different surface structures which result from adsorption of a half monolayer of C, N, or O atoms on the Ni(1 0 0) surface. C or N atoms sit nearly coplanar with the surface Ni atoms and induce the "clock" reconstruction of the surface. In contrast, adsorbed O atoms sit slightly above the Ni(1 0 0) surface plane and have little effect on the overall surface structure. The local environments of the C, N, and O atoms on these surfaces are similar to their environments in a series of late transition metal carbonyl clusters, suggesting that some of the same electronic factors may play a role in favoring the different structures. Results of the calculations indicate that when adsorbates occupy coplanar sites on Ni(1 0 0), much of the Ni-Ni bonding within the surface layer and between the surface- and second-layers is disrupted. On the C- and N-covered surfaces the disruption is more than compensated for by the formation of strong adsorbate-Ni bonds and by new Ni-Ni surface bonds resulting from the clock reconstruction. When O is forced into a coplanar site, however, both the higher electron count and increased electronegativity of the O atoms lead to severe disruption of the surface bonding and weak Ni-O bonds. When O atoms sit above the surface, they form more polar Ni-O bonds, contribute less electron density to the Ni surface bands, and cause less disruption to Ni-Ni surface bonds. These results suggest that, similar to the organometallic clusters, the site preferences of C, N, and O atoms are directly related to their electron count, and in turn to the relative occupation of both Ni-Ni and X-Ni (X=C, N, O) antibonding bands.

Density functional study on structure and stability of bimetallic AuNZn (N<=6) clusters and their cations

NASA Astrophysics Data System (ADS)

Tanaka, Hiromasa; Neukermans, Sven; Janssens, Ewald; Silverans, Roger E.; Lievens, Peter

2003-10-01

A systematic study on the structure and stability of zinc doped gold clusters has been performed by density functional theory calculations. All the lowest-energy isomers found have a planar structure and resemble pure gold clusters in shape. Stable isomers tend to equally delocalize valence s electrons of the constituent atoms over the entire structure and maximize the number of Au-Zn bonds in the structure. This is because the Au-Zn bond is stronger than the Au-Au bond and gives an extra σ-bonding interaction by the overlap between vacant Zn 4p and valence Au 6s(5d) orbitals. No three-dimensional isomers were found for Au5Zn+ and Au4Zn clusters containing six delocalized valence electrons. This result reflects that these clusters have a magic number of delocalized electrons for two-dimensional systems. Calculated vertical ionization energies and dissociation energies as a function of the cluster size show odd-even behavior, in agreement with recent mass spectrometric observations [Tanaka et al., J. Am. Chem. Soc. 125, 2862 (2003)].

Understanding metallic bonding: Structure, process and interaction by Rasch analysis

NASA Astrophysics Data System (ADS)

Cheng, Maurice M. W.; Oon, Pey-Tee

2016-08-01

This paper reports the results of a survey of 3006 Year 10-12 students on their understandings of metallic bonding. The instrument was developed based on Chi's ontological categories of scientific concepts and students' understanding of metallic bonding as reported in the literature. The instrument has two parts. Part one probed into students' understanding of metallic bonding as (a) a submicro structure of metals, (b) a process in which individual metal atoms lose their outermost shell electrons to form a 'sea of electrons' and octet metal cations or (c) an all-directional electrostatic force between delocalized electrons and metal cations, that is, an interaction. Part two assessed students' explanation of malleability of metals, for example (a) as a submicro structural rearrangement of metal atoms/cations or (b) based on all-directional electrostatic force. The instrument was validated by the Rasch Model. Psychometric assessment showed that the instrument possessed reasonably good properties of measurement. Results revealed that it was reliable and valid for measuring students' understanding of metallic bonding. Analysis revealed that the structure, process and interaction understandings were unidimensional and in an increasing order of difficulty. Implications for the teaching of metallic bonding, particular through the use of diagrams, critiques and model-based learning, are discussed.

The Structure and Properties of Diffusion Assisted Bonded Joints in 17-4 PH, Type 347, 15-5 PH and Nitronic 40 Stainless Steels

NASA Technical Reports Server (NTRS)

Wigley, D. A.

1981-01-01

Diffusion assisted bonds are formed in 17-4 PH, 15-5 PH, type 347 and Nitronic 40 stainless steels using electrodeposited copper as the bonding agent. The bonds are analyzed by conventional metallographic, electron microprobe analysis, and scanning electron microscopic techniques as well as Charpy V-notch impact tests at temperatures of 77 and 300 K. Results are discussed in terms of a postulated model for the bonding process.

Electronic structure and bonding of intergranular glassy films in polycrystalline Si3 N4 : Ab initio studies and classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Rulis, P.; Chen, J.; Ouyang, L.; Ching, W.-Y.; Su, X.; Garofalini, S. H.

2005-06-01

The electronic structure and bonding of a realistic model of an intergranular glassy film (IGF) was studied with multiple computational methods. The model has a Si-O-N glassy region sandwiched between crystalline basal planes of β-Si3N4 and contains a total of 798 atoms. It was constructed with periodic boundary conditions via classical molecular dynamics (MD) techniques using an accurate multibody atomic potential. The model was then further relaxed by the VASP (Vienna ab initio simulation package) program. It is shown that the VASP-relaxed structure reduces the total energy from the MD-relaxed structure by only 47.38eV , validating the accuracy of the multiatom potential used. The calculated electronic structure shows the IGF model to be an insulator with a sizable gap of almost 3eV . Quasidefectlike states can be identified near the band edges arising from the more strained Si-N and Si-O bonds at the interface. Calculation of the Mulliken effective charge and bond order values indicates that the bonds in the glassy region and at the interface can be enhanced and weakened by distortions in the bond length and bond angle. The states at the top of the valence band are derived mostly from the crystalline part of the Si-N bonding while the states at the bottom of the conduction band are dominated by the Si-O bonding in the glassy region. Calculation of the electrostatic potential across the interface shows an average band offset of about 1.5eV between the crystalline β-Si3N4 and the glassy Si-O-N region which could be related to the space charge model for IGF.

Single and double carbon vacancies in pyrene as first models for graphene defects: A survey of the chemical reactivity toward hydrogen

NASA Astrophysics Data System (ADS)

Nieman, Reed; Das, Anita; Aquino, Adélia J. A.; Amorim, Rodrigo G.; Machado, Francisco B. C.; Lischka, Hans

2017-01-01

Graphene is regarded as one of the most promising materials for nanoelectronics applications. Defects play an important role in modulating its electronic properties and also enhance its chemical reactivity. In this work the reactivity of single vacancies (SV) and double vacancies (DV) in reaction with a hydrogen atom Hr is studied. Because of the complicated open shell electronic structures of these defects due to dangling bonds, multireference configuration interaction (MRCI) methods are being used in combination with a previously developed defect model based on pyrene. Comparison of the stability of products derived from Csbnd Hr bond formation with different carbon atoms of the different polyaromatic hydrocarbons is made. In the single vacancy case the most stable structure is the one where the incoming hydrogen is bound to the carbon atom carrying the dangling bond. However, stable Csbnd Hr bonded structures are also observed in the five-membered ring of the single vacancy. In the double vacancy, most stable bonding of the reactant Hr atom is found in the five-membered rings. In total, Csbnd Hr bonds, corresponding to local energy minimum structures, are formed with all carbon atoms in the different defect systems and the pyrene itself. Reaction profiles for the four lowest electronic states show in the case of a single vacancy a complex picture of curve crossings and avoided crossings which will give rise to a complex nonadiabatic reaction dynamics involving several electronic states.

ULTRAFAST CHEMISTRY: Using Time-Resolved Vibrational Spectroscopy for Interrogation of Structural Dynamics

NASA Astrophysics Data System (ADS)

Nibbering, Erik T. J.; Fidder, Henk; Pines, Ehud

2005-05-01

Time-resolved infrared (IR) and Raman spectroscopy elucidates molecular structure evolution during ultrafast chemical reactions. Following vibrational marker modes in real time provides direct insight into the structural dynamics, as is evidenced in studies on intramolecular hydrogen transfer, bimolecular proton transfer, electron transfer, hydrogen bonding during solvation dynamics, bond fission in organometallic compounds and heme proteins, cis-trans isomerization in retinal proteins, and transformations in photochromic switch pairs. Femtosecond IR spectroscopy monitors the site-specific interactions in hydrogen bonds. Conversion between excited electronic states can be followed for intramolecular electron transfer by inspection of the fingerprint IR- or Raman-active vibrations in conjunction with quantum chemical calculations. Excess internal vibrational energy, generated either by optical excitation or by internal conversion from the electronic excited state to the ground state, is observable through transient frequency shifts of IR-active vibrations and through nonequilibrium populations as deduced by Raman resonances.

Chapter 5 Multiple, Localized, and Delocalized/Conjugated Bonds in the Orbital Communication Theory of Molecular Systems

NASA Astrophysics Data System (ADS)

Nalewajski, Roman F.

Information theory (IT) probe of the molecular electronic structure, within the communication theory of chemical bonds (CTCB), uses the standard entropy/information descriptors of the Shannon theory of communication to characterize a scattering of the electronic probabilities and their information content throughout the system chemical bonds generated by the occupied molecular orbitals (MO). These "communications" between the basis-set orbitals are determined by the two-orbital conditional probabilities: one- and two-electron in character. They define the molecular information system, in which the electron-allocation "signals" are transmitted between various orbital "inputs" and "outputs". It is argued, using the quantum mechanical superposition principle, that the one-electron conditional probabilities are proportional to the squares of corresponding elements of the charge and bond-order (CBO) matrix of the standard LCAO MO theory. Therefore, the probability of the interorbital connections in the molecular communication system is directly related to Wiberg's quadratic covalency indices of chemical bonds. The conditional-entropy (communication "noise") and mutual-information (information capacity) descriptors of these molecular channels generate the IT-covalent and IT-ionic bond components, respectively. The former reflects the electron delocalization (indeterminacy) due to the orbital mixing, throughout all chemical bonds in the system under consideration. The latter characterizes the localization (determinacy) in the probability scattering in the molecule. These two IT indices, respectively, indicate a fraction of the input information lost in the channel output, due to the communication noise, and its surviving part, due to deterministic elements in probability scattering in the molecular network. Together, these two components generate the system overall bond index. By a straightforward output reduction (condensation) of the molecular channel, the IT indices of molecular fragments, for example, localized bonds, functional groups, and forward and back donations accompanying the bond formation, and so on, can be extracted. The flow of information in such molecular communication networks is investigated in several prototype molecules. These illustrative (model) applications of the orbital communication theory of chemical bonds (CTCB) deal with several classical issues in the electronic structure theory: atom hybridization/promotion, single and multiple chemical bonds, bond conjugation, and so on. The localized bonds in hydrides and delocalized [pi]-bonds in simple hydrocarbons, as well as the multiple bonds in CO and CO2, are diagnosed using the entropy/information descriptors of CTCB. The atom promotion in hydrides and bond conjugation in [pi]-electron systems are investigated in more detail. A major drawback of the previous two-electron approach to molecular channels, namely, two weak bond differentiation in aromatic systems, has been shown to be remedied in the one-electron approach.

Photoelectron spectroscopic study on the electronic structures of the dental gold alloys and their interaction with L-cysteine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ogawa, Koji; Takahashi, Kazutoshi; Azuma, Junpei

The valence electronic structures of the dental gold alloys, type 1, type 3, and K14, and their interaction with L-cysteine have been studied by ultraviolet photoelectron spectroscopy with synchrotron radiation. It was found that the electronic structures of the type-1 and type-3 dental alloys are similar to that of polycrystalline Au, while that of the K14 dental alloy is much affected by Cu. The peak shift and the change in shape due to alloying are observed in all the dental alloys. It is suggested that the new peak observed around 2 eV for the L-cysteine thin films on all themore » dental alloys may be due to the bonding of S 3sp orbitals with the dental alloy surfaces, and the Cu-S bond, as well as the Au-S and Au-O bonds, may cause the change in the electronic structure of the L-cysteine on the alloys.« less

Structure-property relationships in cubic cuprous iodide: A novel view on stability, chemical bonding, and electronic properties

NASA Astrophysics Data System (ADS)

Pishtshev, A.; Karazhanov, S. Zh.

2017-02-01

Based on the combination of density functional theory and theory-group methods, we performed systematic modeling of γ-CuI structural design at the atomistic level. Being started from the metallic copper lattice, we treated a crystal assembly as a stepwise iodination process characterized in terms of a sequence of intermediate lattice geometries. These geometries were selected and validated via screening of possible structural transformations. The genesis of chemical bonding was studied for three structural transformations by analyzing the relevant changes in the topology of valence electron densities. We determined structural trends driven by metal-ligand coupling. This allowed us to suggest the improved scenario of chemical bonding in γ-CuI. In particular, the unconventional effect of spatial separation of metallic and covalent interactions was found to be very important with respect to the preferred arrangements of valence electrons in the iodination process. We rigorously showed that useful electronic and optical properties of γ-CuI originate from the combination of two separated bonding patterns—strong covalency established in I-Cu tetrahedral connections and noncovalent interactions of copper cores is caused by the 3d10 closed-shell electron configurations. The other finding of ours is that the self-consistency of the GW calculations is crucial for correctly determining the dynamic electronic correlations in γ-CuI. Detail reinvestigation of the quasi-particle energy structure by means of the self-consistent GW approach allowed us to explain how p-type electrical conductivity can be engineered in the material.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trump, Benjamin A., E-mail: btrump1@jhu.edu; Department of Physics and Astronomy, Institute for Quantum Matter, Johns Hopkins University, Baltimore, MD 21218; McQueen, Tyrel M., E-mail: mcqueen@jhu.edu

The synthesis and physical properties of the new distorted-Hollandite PbIr{sub 4}Se{sub 8} are reported. Powder X-ray diffraction and transmission electron microscopy show that the structure consists of edge- and corner-sharing IrSe{sub 6} octahedra, with one-dimensional channels occupied by Pb. The structure contains Se-Se anion-anion bonding, leading to an electron count of Pb{sup 2+}(Ir{sup 3+}){sub 4}(Se{sub 2}){sup 2-}(Se{sup 2−}){sub 6}, confirmed by bond-valence sums and diamagnetic behavior. Structural and heat capacity measurements demonstrate disorder on the Pb site, due to the combination of lone-pair effects and the large size of the one-dimensional channels. Comparisons are made to known Hollandite and pseudo-Hollanditemore » structures, which demonstrates that the anion-anion bonding in PbIr{sub 4}Se{sub 8} distorts its structure, to accommodate the Ir{sup 3+} state. An electronic structure calculation indicates semiconductor character with a band gap of 0.76(11) eV.« less

Cluster molecular orbital description of the electronic structures of mixed-valence iron oxides and silicates

USGS Publications Warehouse

Sherman, David M.

1986-01-01

A molecular orbital description, based on spin-unrestricted X??-scattered wave calculations, is given for the electronic structures of mixed valence iron oxides and silicates. The cluster calculations show that electron hopping and optical intervalence charge-transger result from weak FeFe bonding across shared edges of FeO6 coordination polyhedra. In agreement with Zener's double exchange model, FeFe bonding is found to stabilize ferromagnetic coupling between Fe2+ and Fe3+ cations. ?? 1986.

Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis.

PubMed

Zarychta, Bartosz; Lyubimov, Artem; Ahmed, Maqsood; Munshi, Parthapratim; Guillot, Benoît; Vrielink, Alice; Jelsch, Christian

2015-04-01

Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein-cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O···H-N hydrogen bonds was analyzed with respect to the different secondary-structure elements.

Photosynthesis. Electronic structure of the oxygen-evolving complex in photosystem II prior to O-O bond formation.

PubMed

Cox, Nicholas; Retegan, Marius; Neese, Frank; Pantazis, Dimitrios A; Boussac, Alain; Lubitz, Wolfgang

2014-08-15

The photosynthetic protein complex photosystem II oxidizes water to molecular oxygen at an embedded tetramanganese-calcium cluster. Resolving the geometric and electronic structure of this cluster in its highest metastable catalytic state (designated S3) is a prerequisite for understanding the mechanism of O-O bond formation. Here, multifrequency, multidimensional magnetic resonance spectroscopy reveals that all four manganese ions of the catalyst are structurally and electronically similar immediately before the final oxygen evolution step; they all exhibit a 4+ formal oxidation state and octahedral local geometry. Only one structural model derived from quantum chemical modeling is consistent with all magnetic resonance data; its formation requires the binding of an additional water molecule. O-O bond formation would then proceed by the coupling of two proximal manganese-bound oxygens in the transition state of the cofactor. Copyright © 2014, American Association for the Advancement of Science.

Electronic structure and acid-base properties of Kojic acid and its dimers. A DFT and quantum topology study

NASA Astrophysics Data System (ADS)

Aziz, Saadullah G.; Alyoubi, Abdulrahman O.; Elroby, Shaaban A.; Hilal, Rifaat H.

2017-10-01

Kojic acid is a polyfunctional heterocyclic compound, with several important reaction centres; it has a wide range of applications in the cosmetic, medicine, food, agriculture and chemical industries. The present study aims at better insight into its electronic structure and bonding characteristics. Thus, density functional theory at the M06-2x /6-311++G** level of theory is used to investigate its ground state electronic and acid-base properties. Protonation and deprotonation enthalpies are computed and analysed. The ability of Kojic acid to form both water complexes and dimers is explored. Several different complexes and dimer structures were examined. Natural bond order and quantum topology features of the charge density were analysed. The origin of the stability of the studied complexes and dimer structures can be traced to hydrogen bonding, π-conjugative and non-covalent dispersive interactions.

Features of the electronic structure of FeTe compounds

NASA Astrophysics Data System (ADS)

Grechnev, G. E.; Lyogenkaya, A. A.; Panfilov, A. S.; Logosha, A. V.; Kotlyar, O. V.; Gnezdilov, V. P.; Makarova, I. P.; Chareev, D. A.; Mitrofanova, E. S.

2015-12-01

A theoretical and experimental study of the electronic structure and nature of the chemical bonds in FeTe compounds in antiferromagnetic (AFM) and paramagnetic phases was carried out. It is established that the nature of the chemical bonds is mainly metallic, and the presence of covalent bonds Fe-Te and Te-Te helps to stabilize the structural distortions of the tetragonal phase of FeTe in the low-temperature region. It is found that the bicollinear AFM structure corresponds to the ground state of the FeTe compound and the calculated value of the magnetic moment MFe = -2.4μB is in good agreement with the data from neutron diffraction measurements. At the same time, the Fermi surface (FS) of the low-temperature AFM phase is radically different from the FS of the paramagnetic FeTe. Reconstructing the FS can lead to a sign change of the Hall coefficient observed in FeTe. The calculation results serve as evidence of the fact that the electronic structures and magnetic properties of FeTe are well-described by the model of itinerant d-electrons and the density functional theory (DFT-GGA).

Creating a single twin boundary between two CdTe (111) wafers with controlled rotation angle by wafer bonding

NASA Astrophysics Data System (ADS)

Sun, Ce; Lu, Ning; Wang, Jinguo; Lee, Jihyung; Peng, Xin; Klie, Robert F.; Kim, Moon J.

2013-12-01

The single twin boundary with crystallographic orientation relationship (1¯1¯1¯)//(111) [01¯1]//[011¯] was created by wafer bonding. Electron diffraction patterns and high-resolution transmission electron microscopy images demonstrated the well control of the rotation angle between the bonded pair. At the twin boundary, one unit of wurtzite structure was found between two zinc-blende matrices. High-angle annular dark-field scanning transmission electron microscopy images showed Cd- and Te-terminated for the two bonded portions, respectively. The I-V curve across the twin boundary showed increasingly nonlinear behavior, indicating a potential barrier at the bonded twin boundary.

Structural, electronic, elastic, and thermodynamic properties of CaSi, Ca2Si, and CaSi2 phases from first-principles calculations

NASA Astrophysics Data System (ADS)

Li, X. D.; Li, K.; Wei, C. H.; Han, W. D.; Zhou, N. G.

2018-06-01

The structural, electronic, elastic, and thermodynamic properties of CaSi, Ca2Si, and CaSi2 are systematically investigated by using first-principles calculations method based on density functional theory (DFT). The calculated formation enthalpies and cohesive energies show that CaSi2 possesses the greatest structural stability and CaSi has the strongest alloying ability. The structural stability of the three phases is compared according to electronic structures. Further analysis on electronic structures indicates that the bonding of these phases exhibits the combinations of metallic, covalent, and ionic bonds. The elastic constants are calculated, and the bulk modulus, shear modulus, Young's modulus, Poisson's ratio, and anisotropy factor of polycrystalline materials are deduced. Additionally, the thermodynamic properties were theoretically predicted and discussed.

Microstructural evolution and micromechanical properties of gamma-irradiated Au ball bonds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yusoff, Wan Yusmawati Wan, E-mail: yusmawati@upnm.edu.my; Ismail, Roslina, E-mail: roslina.ismail@ukm.my; Jalar, Azman, E-mail: azmn@ukm.my

2014-07-01

The effect of gamma radiation on the mechanical and structural properties of gold ball bonds was investigated. Gold wires from thermosonic wire bonding were exposed to gamma rays from a Cobalt-60 source at a low dose (5 Gy). The load–depth curve of nanoindentation for the irradiated gold wire bond has an apparent staircase shape during loading compared to the as-received sample. The hardness of the specimens calculated from the nanoindentation shows an increase in value from 0.91 to 1.09 GPa for specimens after exposure. The reduced elastic modulus for irradiated specimens significantly increased as well, with values from 75.18 tomore » 98.55 GPa. The change in intrinsic properties due to gamma radiation was investigated using dual-focused ion beam and high-resolution transmission electron microscope analysis. The dual-focused ion beam and high-resolution transmission electron microscope images confirmed the changes in grain structure and the presence of dislocations. The scanning electron microscope micrographs of focused ion beam cross sections showed that the grain structure of the gold became elongated and smaller after exposure to gamma rays. Meanwhile, high-resolution transmission electron microscopy provided evidence that gamma radiation induced dislocation of the atomic arrangement. - Highlights: • Nanoindentation technique provides a detailed characterisation of Au ball bond. • P–h curve of irradiated Au ball bond shows an apparent pop-in event. • Hardness and reduced modulus increased after exposure. • Elongated and smaller grain structure in irradiated specimens • Prevalent presence of dislocations in the atomic arrangement.« less

Teaching Chemistry with Electron Density Models.

ERIC Educational Resources Information Center

Shusterman, Gwendolyn P.; Shusterman, Alan J.

1997-01-01

Describes a method for teaching electronic structure and its relevance to chemical phenomena that relies on computer-generated three-dimensional models of electron density distributions. Discusses the quantum mechanical background needed and presents ways of using models of electronic ground states to teach electronic structure, bonding concepts,…

On the multi-reference nature of plutonium oxides: PuO22+, PuO2, PuO3 and PuO2(OH)2.

PubMed

Boguslawski, Katharina; Réal, Florent; Tecmer, Paweł; Duperrouzel, Corinne; Gomes, André Severo Pereira; Legeza, Örs; Ayers, Paul W; Vallet, Valérie

2017-02-08

Actinide-containing complexes present formidable challenges for electronic structure methods due to the large number of degenerate or quasi-degenerate electronic states arising from partially occupied 5f and 6d shells. Conventional multi-reference methods can treat active spaces that are often at the upper limit of what is required for a proper treatment of species with complex electronic structures, leaving no room for verifying their suitability. In this work we address the issue of properly defining the active spaces in such calculations, and introduce a protocol to determine optimal active spaces based on the use of the Density Matrix Renormalization Group algorithm and concepts of quantum information theory. We apply the protocol to elucidate the electronic structure and bonding mechanism of volatile plutonium oxides (PuO 3 and PuO 2 (OH) 2 ), species associated with nuclear safety issues for which little is known about the electronic structure and energetics. We show how, within a scalar relativistic framework, orbital-pair correlations can be used to guide the definition of optimal active spaces which provide an accurate description of static/non-dynamic electron correlation, as well as to analyse the chemical bonding beyond a simple orbital model. From this bonding analysis we are able to show that the addition of oxo- or hydroxo-groups to the plutonium dioxide species considerably changes the π-bonding mechanism with respect to the bare triatomics, resulting in bent structures with a considerable multi-reference character.

On Substrate for Atomic Chain Electronics

NASA Technical Reports Server (NTRS)

Yamada, Toshishige; Bauschlicher, Charles W., Jr.; Partridge, Harry; Saini, Subhash (Technical Monitor)

1998-01-01

A substrate for future atomic chain electronics, where adatoms are placed at designated positions and form atomically precise device components, is studied theoretically. The substrate has to serve as a two-dimensional template for adatom mounting with a reasonable confinement barrier and also provide electronic isolation, preventing unwanted coupling between independent adatom structures. However, the two requirements conflict. For excellent electronic isolation, we may seek adatom confinement via van der Waals interaction without chemical bonding to the substrate atoms, but the confinement turns out to be very weak and hence unsatisfactory. An alternative chemical bonding scheme with excellent structural strength is examined, but even fundamental adatom chain properties such as whether chains are semiconducting or metallic are strongly influenced by the nature of the chemical bonding, and electronic isolation is not always achieved. Conditions for obtaining semiconducting chains with well-localized surface-modes, leading to good isolation, are clarified and discussed.

Electronic structure description of the cis-MoOS unit in models for molybdenum hydroxylases.

PubMed

Doonan, Christian J; Rubie, Nick D; Peariso, Katrina; Harris, Hugh H; Knottenbelt, Sushilla Z; George, Graham N; Young, Charles G; Kirk, Martin L

2008-01-09

The molybdenum hydroxylases catalyze the oxidation of numerous aromatic heterocycles and simple organics and, unlike other hydroxylases, utilize water as the source of oxygen incorporated into the product. The electronic structures of the cis-MoOS units in CoCp2[TpiPrMoVOS(OPh)] and TpiPrMoVIOS(OPh) (TpiPr = hydrotris(3-isopropylpyrazol-1-yl)borate), new models for molybdenum hydroxylases, have been studied in detail using S K-edge X-ray absorption spectroscopy, vibrational spectroscopy, and detailed bonding calculations. The results show a highly delocalized Mo=S pi* LUMO redox orbital that is formally Mo(dxy) with approximately 35% sulfido ligand character. Vibrational spectroscopy has been used to quantitate Mo-Ssulfido bond order changes in the cis-MoOS units as a function of redox state. Results support a redox active molecular orbital that has a profound influence on MoOS bonding through changes to the relative electro/nucleophilicity of the terminal sulfido ligand accompanying oxidation state changes. The bonding description for these model cis-MoOS systems supports enzyme mechanisms that are under orbital control and dominantly influenced by the unique electronic structure of the cis-MoOS site. The electronic structure of the oxidized enzyme site is postulated to play a role in polarizing a substrate carbon center for nucleophilic attack by metal activated water and acting as an electron sink in the two-electron oxidation of substrates.

Atomic and electronic structures of an extremely fragile liquid.

PubMed

Kohara, Shinji; Akola, Jaakko; Patrikeev, Leonid; Ropo, Matti; Ohara, Koji; Itou, Masayoshi; Fujiwara, Akihiko; Yahiro, Jumpei; Okada, Junpei T; Ishikawa, Takehiko; Mizuno, Akitoshi; Masuno, Atsunobu; Watanabe, Yasuhiro; Usuki, Takeshi

2014-12-18

The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia-Thornton number-number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr-O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr-O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid.

Atomic and electronic structures of an extremely fragile liquid

PubMed Central

Kohara, Shinji; Akola, Jaakko; Patrikeev, Leonid; Ropo, Matti; Ohara, Koji; Itou, Masayoshi; Fujiwara, Akihiko; Yahiro, Jumpei; Okada, Junpei T.; Ishikawa, Takehiko; Mizuno, Akitoshi; Masuno, Atsunobu; Watanabe, Yasuhiro; Usuki, Takeshi

2014-01-01

The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia–Thornton number–number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr–O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr–O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid. PMID:25520236

Maxima of |Ψ|2: a connection between quantum mechanics and Lewis structures.

PubMed

Lüchow, Arne

2014-04-30

The maxima of squared electronic wave functions |Ψ|2 are analyzed for a number of small molecules. They are in principle observables and show considerable chemical insight from first principles. The maxima contain substantial information about the relative electron positions in a molecule, such as the pairing of opposite spin electrons and the Pauli repulsion which are lost in the electron density. Single bond and double bond as well as polar bond pairs and lone pairs are obtained from the maximum analysis. In many cases, we find a correspondence to the electron arrangements in molecules as assumed by Lewis in 1916. Copyright © 2014 Wiley Periodicals, Inc.

Electron detachment of the hydrogen-bonded amino acid side-chain guanine complexes

NASA Astrophysics Data System (ADS)

Wang, Jing; Gu, Jiande; Leszczynski, Jerzy

2007-07-01

The photoelectron spectra of the hydrogen-bonded amino acid side-chain-guanine complexes has been studied at the partial third order (P3) self-energy approximation of the electron propagator theory. The correlation between the vertical electron detachment energy and the charge distributions on the guanine moiety reveals that the vertical electron detachment energy (VDE) increases as the positive charge distribution on the guanine increases. The low VDE values determined for the negatively charged complexes of the guanine-side-chain-group of Asp/Glu suggest that the influence of the H-bonded anionic groups on the VDE of guanine could be more important than that of the anionic backbone structure. The even lower vertical electron detachment energy for guanine is thus can be expected in the H-bonded protein-DNA systems.

Photoelectron spectroscopy of B4O4-: Dual 3c-4e π hyperbonds and rhombic 4c-4e o-bond in boron oxide clusters

NASA Astrophysics Data System (ADS)

Tian, Wen-Juan; Zhao, Li-Juan; Chen, Qiang; Ou, Ting; Xu, Hong-Guang; Zheng, Wei-Jun; Zhai, Hua-Jin; Li, Si-Dian

2015-04-01

Gas-phase anion photoelectron spectroscopy (PES) is combined with global structural searches and electronic structure calculations at the hybrid Becke 3-parameter exchange functional and Lee-Yang-Parr correlation functional (B3LYP) and single-point coupled-cluster with single, double, and perturbative triple excitations (CCSD(T)) levels to probe the structural and electronic properties and chemical bonding of the B4O40/- clusters. The measured PES spectra of B4O4- exhibit a major band with the adiabatic and vertical detachment energies (ADE and VDE) of 2.64 ± 0.10 and 2.81 ± 0.10 eV, respectively, as well as a weak peak with the ADE and VDE of 1.42 ± 0.08 and 1.48 ± 0.08 eV. The former band proves to correspond to the Y-shaped global minimum of Cs B4O4- (2A″), with the calculated ADE/VDE of 2.57/2.84 eV at the CCSD(T) level, whereas the weak band is associated with the second lowest-energy, rhombic isomer of D2h B4O4- (2B2g) with the predicted ADE/VDE of 1.43/1.49 eV. Both anion structures are planar, featuring a B atom or a B2O2 core bonded with terminal BO and/or BO2 groups. The same Y-shaped and rhombic structures are also located for the B4O4 neutral cluster, albeit with a reversed energy order. Bonding analyses reveal dual three-center four-electron (3c-4e) π hyperbonds in the Y-shaped B4O40/- clusters and a four-center four-electron (4c-4e) π bond, that is, the so-called o-bond in the rhombic B4O40/- clusters. This work is the first experimental study on a molecular system with an o-bond.

Supramolecularly engineered perylene bisimide assemblies exhibiting thermal transition from columnar to multilamellar structures.

PubMed

Yagai, Shiki; Usui, Mari; Seki, Tomohiro; Murayama, Haruno; Kikkawa, Yoshihiro; Uemura, Shinobu; Karatsu, Takashi; Kitamura, Akihide; Asano, Atsushi; Seki, Shu

2012-05-09

Perylene 3,4:9,10-tetracarboxylic acid bisimide (PBI) was functionalized with ditopic cyanuric acid to organize it into complex columnar architectures through the formation of hydrogen-bonded supermacrocycles (rosette) by complexing with ditopic melamines possessing solubilizing alkoxyphenyl substituents. The aggregation study in solution using UV-vis and NMR spectroscopies showed the formation of extended aggregates through hydrogen-bonding and π-π stacking interactions. The cylindrical fibrillar nanostructures were visualized by microscopic techniques (AFM, TEM), and the formation of lyotropic mesophase was confirmed by polarized optical microscopy and SEM. X-ray diffraction study revealed that a well-defined hexagonal columnar (Col(h)) structure was formed by solution-casting of fibrillar assemblies. All of these results are consistent with the formation of hydrogen-bonded PBI rosettes that spontaneously organize into the Col(h) structure. Upon heating the Col(h) structure in the bulk state, a structural transition to a highly ordered lamellar (Lam) structure was observed by variable-temperature X-ray diffraction, differential scanning calorimetry, and AFM studies. IR study showed that the rearrangement of the hydrogen-bonding motifs occurs during the structural transition. These results suggest that such a striking structural transition is aided by the reorganization in the lowest level of self-organization, i.e., the rearrangement of hydrogen-bonded motifs from rosette to linear tape. A remarkable increase in the transient photoconductivity was observed by the flash-photolysis time-resolved microwave conductivity (FP-TRMC) measurements upon converting the Col(h) structure to the Lam structure. Transient absorption spectroscopy revealed that electron transfer from electron-donating alkoxyphenyl groups of melamine components to electron-deficient PBI moieties takes place, resulting in a higher probability of charge carrier generation in the Lam structure compared to the Col(h) structure.

Lattice structures and electronic properties of MO/MoSe2 interface from first-principles calculations

NASA Astrophysics Data System (ADS)

Zhang, Yu; Tang, Fu-Ling; Xue, Hong-Tao; Lu, Wen-Jiang; Liu, Jiang-Fei; Huang, Min

2015-02-01

Using first-principles plane-wave calculations within density functional theory, we theoretically studied the atomic structure, bonding energy and electronic properties of the perfect Mo (110)/MoSe2 (100) interface with a lattice mismatch less than 4.2%. Compared with the perfect structure, the interface is somewhat relaxed, and its atomic positions and bond lengths change slightly. The calculated interface bonding energy is about -1.2 J/m2, indicating that this interface is very stable. The MoSe2 layer on the interface has some interface states near the Fermi level, the interface states are mainly caused by Mo 4d orbitals, while the Se atom almost have no contribution. On the interface, Mo-5s and Se-4p orbitals hybridize at about -6.5 to -5.0 eV, and Mo-4d and Se-4p orbitals hybridize at about -5.0 to -1.0 eV. These hybridizations greatly improve the bonding ability of Mo and Se atom in the interface. By Bader charge analysis, we find electron redistribution near the interface which promotes the bonding of the Mo and MoSe2 layer.

Electronic structure, chemical bonding, and geometry of pure and Sr-doped CaCO3.

PubMed

Stashans, Arvids; Chamba, Gaston; Pinto, Henry

2008-02-01

The electronic structure, chemical bonding, geometry, and effects produced by Sr-doping in CaCO(3) have been studied on the basis of density-functional theory using the VASP simulation package and molecular-orbital theory utilizing the CLUSTERD computer code. Two calcium carbonate structures which occur naturally in anhydrous crystalline forms, calcite and aragonite, were considered in the present investigation. The obtained diagrams of density of states show similar patterns for both materials. The spatial structures are computed and analyzed in comparison to the available experimental data. The electronic properties and atomic displacements because of the trace element Sr-incorporation are discussed in a comparative manner for the two crystalline structures. (c) 2007 Wiley Periodicals, Inc.

Core-level photoabsorption study of defects and metastable bonding configurations in boron nitride

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jimenez, I.; Jankowski, A.F.; Terminello, L.J.

1997-04-01

Boron nitride is an interesting material for technological applications and for fundamental solid state physics investigations. It is a compound isoelectronic with carbon and, like carbon can possess sp{sup 2} and sp{sup 3} bonded phases resembling graphite and diamond. BN crystallizes in the sp{sup 2}-bonded hexagonal (h-BN), rhombohedral (r-BN) and turbostratic phases, and in the sp{sup 3}-bonded cubic (c-BN) and wurtzite (w-BN) phases. A new family of materials is obtained when replacing C-C pairs in graphite with isoelectronic B-N pairs, resulting in C{sub 2}BN compounds. Regarding other boron compounds, BN is exceptional in the sense that it has standard two-centermore » bonds with conventional coordination numbers, while other boron compounds (e.g. B{sub 4}C) are based on the boron icosahedron unit with three-center bonds and high coordination numbers. The existence of several allotropic forms and fullerene-like structures for BN suggests a rich variety of local bonding and poses the questions of how this affects the local electronic structure and how the material accommodates the stress induced in the transition regions between different phases. One would expect point defects to play a crucial role in stress accommodation, but these must also have a strong influence in the electronic structure, since the B-N bond is polar and a point defect will thus be a charged structure. The study of point defects in relationship to the electronic structure is of fundamental interest in these materials. Recently, the authors have shown that Near-Edge X-ray Absorption Fine Structure (NEXAFS) is sensitive to point defects in h-BN, and to the formation of metastable phases even in amorphous materials. This is significant since other phase identification techniques like vibrational spectroscopies or x-ray diffraction yield ambiguous results for nanocrystalline and amorphous samples. Serendipitously, NEXAFS also combines chemical selectivity with point defect sensitivity.« less

Chemical Bonding in Sulfide Minerals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vaughan, David J.; Rosso, Kevin M.

An understanding of chemical bonding and electronic structure in sulfide minerals is central to any attempt at understanding their crystal structures, stabilities and physical properties. It is also an essential precursor to understanding reactivity through modeling surface structure at the molecular scale. In recent decades, there have been remarkable advances in first principles (ab initio) methods for the quantitative calculation of electronic structure. These advances have been made possible by the very rapid development of high performance computers. Several review volumes that chart the applications of these developments in mineralogy and geochemistry are available (Tossell and Vaughan, 1992; Cygan andmore » Kubicki, 2001). An important feature of the sulfide minerals is the diversity of their electronic structures, as evidenced by their electrical and magnetic properties (see Pearce et al. 2006, this volume). Thus, sulfide minerals range from insulators through semiconductors to metals, and exhibit every type of magnetic behavior. This has presented problems for those attempting to develop bonding models for sulfides, and also led to certain misconceptions regarding the kinds of models that may be appropriate. In this chapter, chemical bonding and electronic structure models for sulfides are reviewed with emphasis on more recent developments. Although the fully ab initio quantitative methods are now capable of a remarkable degree of sophistication in terms of agreement with experiment and potential to interpret and predict behavior with varying conditions, both qualitative and more simplistic quantitative approaches will also be briefly discussed. This is because we believe that the insights which they provide are still helpful to those studying sulfide minerals. In addition to the application of electronic structure models and calculations to solid sulfides, work on sulfide mineral surfaces (Rosso and Vaughan 2006a,b) and solution complexes and clusters (Rickard and Luther, 2006) are discussed in detail later in this volume.« less

Ground/bonding for Large Space System Technology (LSST). [of metallic and nonmetallic structures

NASA Technical Reports Server (NTRS)

Dunbar, W. G.

1980-01-01

The influence of the environment and extravehicular activity remote assembly operations on the grounding and bonding of metallic and nonmetallic structures is discussed. Grounding and bonding philosophy is outlined for the electrical systems and electronic compartments which contain high voltage, high power electrical and electronic equipment. The influence of plasma and particulate on the system was analyzed and the effects of static buildup on the spacecraft electrical system discussed. Conceptual grounding bonding designs are assessed for capability to withstand high current arcs to ground from a high voltage conductor and electromagnetic interference. Also shown were the extravehicular activities required of the space station and or supply spacecraft crew members to join and inspect the ground system using manual on remote assembly construction.

First principles study of the electronic and magnetic structures and bonding properties of UCoC2 ternary, characteristic of C-C units

NASA Astrophysics Data System (ADS)

Matar, Samir F.

2013-03-01

The electronic structure of UCoC2, a di-carbide with the C-C units is examined from ab initio with an assessment of the properties of chemical bonding. The energy-volume equation of state shows large anisotropy effects due to C-C alignment along tetragonal c-axis leading to high linear incompressibility. Relevant features of selective bonding of uranium and cobalt with carbon at two different Wyckoff sites and strong C-C interactions are remarkable. The vibrational frequencies for C⋯C stretching modes indicate closer behavior to aliphatic C-C rather than Cdbnd C double bond. A ferromagnetic ground state is proposed from the calculations.

Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

PubMed

Mondal, Abhisek; Datta, Saumen

2017-06-01

Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Ab initio investigation of the structural and electronic properties of amorphous HgTe.

PubMed

Zhao, Huxian; Chen, Xiaoshuang; Lu, Jianping; Shu, Haibo; Lu, Wei

2014-01-29

We present the structure and electronic properties of amorphous mercury telluride obtained from first-principle calculations. The initial configuration of amorphous mercury telluride is created by computation alchemy. According to different exchange–correlation functions in our calculations, we establish two 256-atom models. The topology of both models is analyzed in terms of radial and bond angle distributions. It is found that both the Te and the Hg atoms tend to be fourfold, but with a wrong bond rate of about 10%. The fraction of threefold and fivefold atoms also shows that there are a significant number of dangling and floating bonds in our models. The electronic properties are also obtained. It is indicated that there is a bandgap in amorphous HgTe, in contrast to the zero bandgap for crystalline HgTe. The structures of the band tail and defect states are also discussed.

Insights into the Electronic Structure of Ozone and Sulfur Dioxide from Generalized Valence Bond Theory: Bonding in O3 and SO2.

PubMed

Takeshita, Tyler Y; Lindquist, Beth A; Dunning, Thom H

2015-07-16

There are many well-known differences in the physical and chemical properties of ozone (O3) and sulfur dioxide (SO2). O3 has longer and weaker bonds than O2, whereas SO2 has shorter and stronger bonds than SO. The O-O2 bond is dramatically weaker than the O-SO bond, and the singlet-triplet gap in SO2 is more than double that in O3. In addition, O3 is a very reactive species, while SO2 is far less so. These disparities have been attributed to variations in the amount of diradical character in the two molecules. In this work, we use generalized valence bond (GVB) theory to characterize the electronic structure of ozone and sulfur dioxide, showing O3 does indeed possess significant diradical character, whereas SO2 is effectively a closed shell molecule. The GVB results provide critical insights into the genesis of the observed difference in these two isoelectronic species. SO2 possesses a recoupled pair bond dyad in the a"(π) system, resulting in SO double bonds. The π system of O3, on the other hand, has a lone pair on the central oxygen atom plus a pair of electrons in orbitals on the terminal oxygen atoms that give rise to a relatively weak π interaction.

Molecules Without Atoms

NASA Astrophysics Data System (ADS)

Ruth, Anthony; Collins, Laura; Gomes, Kenjiro; Janko, Boldizsar

We present a real-space representation of molecules which results in the normal bonding rules and electronic structure of chemistry without atom-centered coulomb potentials. Using a simple mapping, we can generate atomless molecules from the structure of real molecules. Additionally, molecules without atoms show similar covalent bonding energies and transfer of charge in ionic bonds as real molecules. The atomless molecules contain only the valence and conduction electronic structure of the real molecule. Using the framework of the Atoms in Molecules (AIM) theory of Bader, we prove that the topological features of the valence charge distribution of molecules without atoms are identical to that of real molecules. In particular, the charge basins of atomless molecules show identical location and quantities of representative charge. We compare the accuracy, computational cost, and intuition gained from electronic structure calculations of molecules without atoms with the use of pseudopotentials to represent atomic cores in density functional theory. A. R. acknowledges support from a NASA Space Technology Research Fellowship.

Soft X-ray emission spectroscopy of liquids and lithium batterymaterials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Augustsson, Andreas

2004-01-01

Lithium ion insertion into electrode materials is commonly used in rechargeable battery technology. The insertion implies changes in both the crystal structure and the electronic structure of the electrode material. Side-reactions may occur on the surface of the electrode which is exposed to the electrolyte and form a solid electrolyte interface (SEI). The understanding of these processes is of great importance for improving battery performance. The chemical and physical properties of water and alcohols are complicated by the presence of strong hydrogen bonding. Various experimental techniques have been used to study geometrical structures and different models have been proposed tomore » view the details of how these liquids are geometrically organized by hydrogen bonding. However, very little is known about the electronic structure of these liquids, mainly due to the lack of suitable experimental tools. In this thesis examples of studies of lithium battery electrodes and liquid systems using soft x-ray emission spectroscopy will be presented. Monochromatized synchrotron radiation has been used to accomplish selective excitation, in terms of energy and polarization. The electronic structure of graphite electrodes has been studied, before and after lithium intercalation. Changes in the electronic structure upon lithiation due to transfer of electrons into the graphite π-bands have been observed. Transfer of electrons in to the 3d states of transition metal oxides upon lithiation have been studied, through low energy excitations as dd- and charge transfer-excitations. A SEI was detected on cycled graphite electrodes. By the use of selective excitation different carbon sites were probed in the SEI. The local electronic structure of water, methanol and mixtures of the two have been examined using a special liquid cell, to separate the liquid from the vacuum in the experimental chamber. Results from the study of liquid water showed a strong influence on the 3a1 molecular orbital and orbital mixing between water molecules upon hydrogen bonding. Apart from the four-hydrogen-bonding structure in water, a structure where one hydrogen bond is broken could be separated and identified. The soft x-ray emission study of methanol showed the existence of ring and chain formations in the liquid phase and the dominating structures are formed of 6 and 8 molecules. Upon mixing of the two liquids, a segregation at the molecular level was found and the formation of new structures, which could explain the unexpected low increase of the entropy.« less

Short and medium range structures of 80GeSe2–20Ga2Se3 chalcogenide glasses

NASA Astrophysics Data System (ADS)

Petracovschi, Elena; Calvez, Laurent; Cormier, Laurent; Le Coq, David; Du, Jincheng

2018-05-01

The short and medium range structures of 80GeSe2–20Ga2Se3 (or Ge23.5Ga11.8Se64.7) chalcogenide glasses have been studied by combining ab initio molecular dynamics (AIMD) simulations and experimental neutron diffraction studies. The structure factor and total correlation function were calculated from glass structures generated from AIMD simulations and compared with neutron diffraction experiments showing reasonable agreement. The atomic structures of ternary chalcogenide glasses were analyzed in detail, and it was found that gallium atoms are four-fold coordinated by selenium (Se) and form [GaSe4] tetrahedra. Germanium atoms on average also have four-fold coordination, among which Se is 3.5 with the remaining being Ge–Ge homo-nuclear bonds. Ga and Ge tetrahedra link together mainly through corner-sharing and some edge-sharing of Se. No homo-nuclear bonds were observed among Ga atoms or between Ge and Ga. In addition, Se–Se homo-nuclear bonds and Se chains with various lengths were observed. A small fraction of Se atom triclusters that bond to three cations of Ge and Ga were also observed, confirming earlier proposals from 77Se solid state nuclear magnetic resonance studies. Furthermore, the electronic structures of ternary chalcogenide glasses were studied in terms of atomic charge and electronic density of states in order to gain insights into the chemical bonding and electronic properties, as well as to provide an explanation of the observed atomic structures in these ternary chalcogenide glasses.

Tug-of-war between classical and multicenter bonds in H-(Be)n-H species

NASA Astrophysics Data System (ADS)

Lundell, Katie A.; Boldyrev, Alexander I.

2018-05-01

Quantum chemical calculations were performed for beryllium homocatenated compounds [H-(Be)n-H]. Global minimum structures were found using machine searches (Coalescence Kick method) with density functional theory. Chemical bonding analysis was performed with the Adaptive Natural Density Partitioning method. It was found that H-(Be)2-H and H-(Be)3-H clusters are linear with classical two-center two-electron bonds, while for n > 3, three-dimensional structures are more stable with multicenter bonding. Thus, at n = 4, multicenter bonding wins the tug-of-war vs. the classical bonding.

Bonding Diamond To Metal In Electronic Circuits

NASA Technical Reports Server (NTRS)

Jacquez, Andrew E.

1993-01-01

Improved technique for bonding diamond to metal evolved from older technique of soldering or brazing and more suitable for fabrication of delicate electronic circuits. Involves diffusion bonding, developed to take advantage of electrically insulating, heat-conducting properties of diamond, using small diamond bars as supports for slow-wave transmission-line structures in traveling-wave-tube microwave amplifiers. No fillets or side coats formed because metal bonding strips not melted. Technique also used to mount such devices as transistors and diodes electrically insulated from, but thermally connected to, heat sinks.

Electronic structure studies of a clock-reconstructed Al/Pd(1 0 0) surface alloy

NASA Astrophysics Data System (ADS)

Kirsch, Janet E.; Tainter, Craig J.

We have employed solid-state Fenske-Hall band structure calculations to examine the electronic structure of Al/Pd(1 0 0), a surface alloy that undergoes a reconstruction, or rearrangement, of the atoms in the top few surface layers. Surface alloys are materials that consist primarily of a single elemental metal, but which have a bimetallic surface composition that is only a few atomic layers in thickness. The results of this study indicate that reconstruction into a clock configuration simultaneously optimizes the intralayer bonding within the surface plane and the bonding between the first and second atomic layers. These results also allow us to examine the fundamental relationship between the electronic and physical structures of this reconstructed surface alloy.

5-Amino-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde hemihydrate: a polarized electronic structure within hydrogen-bonded sheets of R(10)(8)(34) rings.

PubMed

Quiroga, Jairo; Trilleras, Jorge; Cobo, Justo; Glidewell, Christopher

2010-01-01

In the title compound, C(11)H(11)N(3)O.0.5H(2)O, the water molecule lies across a twofold rotation axis in the space group Pbcn. The bond distances in the organic component provide evidence for polarization of the electronic structure. The molecular components are linked into puckered sheets of R(10)(8)(34) rings by a combination of O-H...N and N-H...O hydrogen bonds; adjacent sheets are weakly linked by an aromatic pi-pi stacking interaction. Comparisons are made with some fused-ring analogues.

Real-space identification of intermolecular bonding with atomic force microscopy.

PubMed

Zhang, Jun; Chen, Pengcheng; Yuan, Bingkai; Ji, Wei; Cheng, Zhihai; Qiu, Xiaohui

2013-11-01

We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.

Atomic and electronic basis for the serrations of refractory high-entropy alloys

NASA Astrophysics Data System (ADS)

Wang, William Yi; Shang, Shun Li; Wang, Yi; Han, Fengbo; Darling, Kristopher A.; Wu, Yidong; Xie, Xie; Senkov, Oleg N.; Li, Jinshan; Hui, Xi Dong; Dahmen, Karin A.; Liaw, Peter K.; Kecskes, Laszlo J.; Liu, Zi-Kui

2017-06-01

Refractory high-entropy alloys present attractive mechanical properties, i.e., high yield strength and fracture toughness, making them potential candidates for structural applications. Understandings of atomic and electronic interactions are important to reveal the origins for the formation of high-entropy alloys and their structure-dominated mechanical properties, thus enabling the development of a predictive approach for rapidly designing advanced materials. Here, we report the atomic and electronic basis for the valence-electron-concentration-categorized principles and the observed serration behavior in high-entropy alloys and high-entropy metallic glass, including MoNbTaW, MoNbVW, MoTaVW, HfNbTiZr, and Vitreloy-1 MG (Zr41Ti14Cu12.5Ni10Be22.5). We find that the yield strengths of high-entropy alloys and high-entropy metallic glass are a power-law function of the electron-work function, which is dominated by local atomic arrangements. Further, a reliance on the bonding-charge density provides a groundbreaking insight into the nature of loosely bonded spots in materials. The presence of strongly bonded clusters and weakly bonded glue atoms imply a serrated deformation of high-entropy alloys, resulting in intermittent avalanches of defects movement.

The Eighteen-Electron Rule

ERIC Educational Resources Information Center

Mitchell, P. R.; Parish, R. V.

1969-01-01

Discusses the stability of the structures of transition metal complexes (primarily carbonyls and organometallic compounds) having 18 electrons or less in their valence shell. Presents molecular orbital diagrams for various structures involving alpha and pi bonding and describes the conditions under which the 18 electron rule applies. (RR)

A quantum chemical study of the structures, stability, and spectroscopy of halogen- and hydrogen-boned complexes between cyanoacetaldehyde and hypochlorous acids

NASA Astrophysics Data System (ADS)

Tang, Qingjie; Guo, Zhenfu; Li, Qingzhong

2014-03-01

The complexes of cyanoacetaldehyde and hypohalous acid (HOX, X = Cl, Br, and I) have been investigated. They can form six different structures (A, B, C, D, E, and F), the former three structures are mainly combined through a N(O)⋯X halogen bond and the latter three structures are maintained mainly by a N(O)⋯H hydrogen bond, although other weaker interactions are also present in most structures. The hydrogen-bonded structures are more stable than the respective halogen-bonded structures. The Osbnd H and Osbnd X bonds in the halogen- and hydrogen-bonded complexes are lengthened and show an observed red shift, while those in the weaker secondary interactions are contracted and display a small blue shift. The orbital interactions in NBO analysis and the electron densities in AIM analysis provide useful and reliable information for the strength of each type of interaction in different structures.

Atomic scale structure and chemistry of interfaces by Z-contrast imaging and electron energy loss spectroscopy in the STEM

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGibbon, M.M.; Browning, N.D.; Chisholm, M.F.

The macroscopic properties of many materials are controlled by the structure and chemistry at the grain boundaries. A basic understanding of the structure-property relationship requires a technique which probes both composition and chemical bonding on an atomic scale. The high-resolution Z-contrast imaging technique in the scanning transmission electron microscope (STEM) forms an incoherent image in which changes in atomic structure and composition can be interpreted intuitively. This direct image allows the electron probe to be positioned over individual atomic columns for parallel detection electron energy loss spectroscopy (PEELS) at a spatial resolution approaching 0.22nm. The bonding information which can bemore » obtained from the fine structure within the PEELS edges can then be used in conjunction with the Z-contrast images to determine the structure at the grain boundary. In this paper we present 3 examples of correlations between the structural, chemical and electronic properties at materials interfaces in metal-semiconductor systems, superconducting and ferroelectric materials.« less

Connecting Dopant Bond Type with Electronic Structure in N-Doped Graphene

DTIC Science & Technology

2012-06-29

dopant forms one σ-bond with its C neighbor, forms σ-bonds to two H (or one N-lone-pair orbital in the unhydrogenated case). Two electrons go into the...pyridinic groups (Table 1), the additional charge from nitrogen is forced to go to the extended carbon π-network, essentially neutralizing the p-doping...T.; Bouchet-Fabre, B.; Granier, A.; Turban, G. XPS and NEXAFS characterisation of plasma deposited vertically aligned N-doped MWCNT . Diamond Relat

The two faces of hydrogen-bond strength on triple AAA-DDD arrays.

PubMed

Lopez, Alfredo Henrique Duarte; Caramori, Giovanni Finoto; Coimbra, Daniel Fernando; Parreira, Renato Luis Tame; da Silva, Éder Henrique

2013-12-02

Systems that are connected through multiple hydrogen bonds are the cornerstone of molecular recognition processes in biology, and they are increasingly being employed in supramolecular chemistry, specifically in molecular self-assembly processes. For this reason, the effects of different substituents (NO2, CN, F, Cl, Br, OCH3 and NH2) on the electronic structure, and consequently on the magnitude of hydrogen bonds in triple AAA-DDD arrays (A=acceptor, D=donor) were evaluated in the light of topological [electron localization function (ELF) and quantum theory of atoms in molecules (QTAIM)], energetic [Su-Li energy-decomposition analysis (EDA) and natural bond orbital analysis (NBO)], and geometrical analysis. The results based on local H-bond descriptors (geometries, QTAIM, ELF, and NBO) indicate that substitutions with electron-withdrawing groups on the AAA module tend to strengthen, whereas electron-donating substituents tend to weaken the covalent character of the AAA-DDD intermolecular H-bonds, and also indicate that the magnitude of the effect is dependent on the position of substitution. In contrast, Su-Li EDA results show an opposite behavior when compared to local H-bond descriptors, indicating that electron-donating substituents tend to increase the magnitude of H-bonds in AAA-DDD arrays, and thus suggesting that the use of local H-bond descriptors describes the nature of H bonds only partially, not providing enough insight about the strength of such H bonds. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The near ultraviolet photodissociation dynamics of 2- and 3-substituted thiophenols: Geometric vs. electronic structure effects

NASA Astrophysics Data System (ADS)

Marchetti, Barbara; Karsili, Tolga N. V.; Cipriani, Maicol; Hansen, Christopher S.; Ashfold, Michael N. R.

2017-07-01

The near ultraviolet spectroscopy and photodissociation dynamics of two families of asymmetrically substituted thiophenols (2- and 3-YPhSH, with Y = F and Me) have been investigated experimentally (by H (Rydberg) atom photofragment translational spectroscopy) and by ab initio electronic structure calculations. Photoexcitation in all cases populates the 11ππ* and/or 11πσ* excited states and results in S-H bond fission. Analyses of the experimentally obtained total kinetic energy release (TKER) spectra yield the respective parent S-H bond strengths, estimates of ΔE(A ˜ -X ˜ ), the energy splitting between the ground (X ˜ ) and first excited (A ˜ ) states of the resulting 2-(3-)YPhS radicals, and reveal a clear propensity for excitation of the C-S in-plane bending vibration in the radical products. The companion theory highlights roles for both geometric (e.g., steric effects and intramolecular H-bonding) and electronic (i.e., π (resonance) and σ (inductive)) effects in determining the respective parent minimum energy geometries, and the observed substituent and position-dependent trends in S-H bond strength and ΔE(A ˜ -X ˜ ). 2-FPhSH shows some clear spectroscopic and photophysical differences. Intramolecular H-bonding ensures that most 2-FPhSH molecules exist as the syn rotamer, for which the electronic structure calculations return a substantial barrier to tunnelling from the photoexcited 11ππ* state to the 11πσ* continuum. The 11ππ* ← S0 excitation spectrum of syn-2-FPhSH thus exhibits resolved vibronic structure, enabling photolysis studies with a greater parent state selectivity. Structure apparent in the TKER spectrum of the H + 2-FPhS products formed when exciting at the 11ππ* ← S0 origin is interpreted by assuming unintended photoexcitation of an overlapping resonance associated with syn-2-FPhSH(v33 = 1) molecules. The present data offer tantalising hints that such out-of-plane motion influences non-adiabatic coupling in the vicinity of a conical intersection (between the 11πσ* and ground state potentials at extended S-H bond lengths) and thus the electronic branching in the eventual radical products.

Stability and electronic structure of the low- Σ grain boundaries in CdTe: a density functional study

DOE PAGES

Park, Ji-Sang; Kang, Joongoo; Yang, Ji-Hui; ...

2015-01-15

Using first-principles density functional calculations, we investigate the relative stability and electronic structure of the grain boundaries (GBs) in zinc-blende CdTe. Among the low-Σ-value symmetric tilt Σ3 (111), Σ3 (112), Σ5 (120), and Σ5 (130) GBs, we show that the Σ3 (111)GB is always the most stable due to the absence of dangling bonds and wrong bonds. The Σ5 (120) GBs, however, are shown to be more stable than the Σ3 (112) GBs, even though the former has a higher Σ value, and the latter is often used as a model system to study GB effects in zinc-blende semiconductors. Furthermore,more » we find that although containing wrong bonds, the Σ5 (120) GBs are electrically benign due to the short wrong bond lengths, and thus are not as harmful as the Σ3 (112) GBs also having wrong bonds but with longer bond lengths.« less

Mo-Mo Quintuple Bond is Highly Reactive in H-H, C-H, and O-H σ-Bond Cleavages Because of the Polarized Electronic Structure in Transition State.

PubMed

Chen, Yue; Sakaki, Shigeyoshi

2017-04-03

The recently reported high reactivity of the Mo-Mo quintuple bond of Mo 2 (N ∧ N) 2 (1) {N ∧ N = μ-κ 2 -CH[N(2,6-iPr 2 C 6 H 3 )] 2 } in the H-H σ-bond cleavage was investigated. DFT calculations disclosed that the H-H σ-bond cleavage by 1 occurs with nearly no barrier to afford the cis-dihydride species followed by cis-trans isomerization to form the trans-dihydride product, which is consistent with the experimental result. The O-H and C-H bond cleavages by 1 were computationally predicted to occur with moderate (ΔG° ⧧ = 9.0 kcal/mol) and acceptable activation energies (ΔG° ⧧ = 22.5 kcal/mol), respectively, suggesting that the Mo-Mo quintuple bond can be applied to various σ-bond cleavages. In these σ-bond cleavage reactions, the charge-transfer (CT Mo→XH ) from the Mo-Mo quintuple bond to the X-H (X = H, C, or O) bond and that (CT XH→Mo ) from the X-H bond to the Mo-Mo bond play crucial roles. Though the HOMO (dδ-MO) of 1 is at lower energy and the LUMO + 2 (dδ*-MO) of 1 is at higher energy than those of RhCl(PMe 3 ) 2 (LUMO and LUMO + 1 of 1 are not frontier MO), the H-H σ-bond cleavage by 1 more easily occurs than that by the Rh complex. Hence, the frontier MO energies are not the reason for the high reactivity of 1. The high reactivity of 1 arises from the polarization of dδ-type MOs of the Mo-Mo quintuple bond in the transition state. Such a polarized electronic structure enhances the bonding overlap between the dδ-MO of the Mo-Mo bond and the σ*-antibonding MO of the X-H bond to facilitate the CT Mo→XH and reduce the exchange repulsion between the Mo-Mo bond and the X-H bond. This polarized electronic structure of the transition state is similar to that of a frustrated Lewis pair. The easy polarization of the dδ-type MOs is one of the advantages of the metal-metal multiple bond, because such polarization is impossible in the mononuclear metal complex.

Electronic structure, elasticity, bonding features and mechanical behaviour of zinc intermetallics: A DFT study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fatima, Bushra, E-mail: bushrafatima25@gmail.com; Acharya, Nikita; Sanyal, Sankar P.

2016-05-06

The structural stability, electronic structure, elastic and mechanical properties of TiZn and ZrZn intermetallics have been studied using ab-initio full potential linearized augmented plane wave (FP-LAPW) method within generalized gradient approximation for exchange and correlation potentials. The various structural parameters, such as lattice constant (a{sub 0}), bulk modulus (B), and its pressure derivative (B’) are analysed and compared. The investigation of elastic constants affirm that both TiZn and ZrZn are elastically stable in CsCl (B{sub 2} phase) structure. The electronic structures have been analysed quantitatively from the band structure which reveals the metallic nature of these compounds. To better illustratemore » the nature of bonding and charge transfer, we have also studied the Fermi surfaces. The three well known criterion of ductility namely Pugh’s rule, Cauchy’s pressure and Frantsevich rule elucidate the ductile nature of these compounds.« less

Photoelectron spectroscopy of B4O4 (-): Dual 3c-4e π hyperbonds and rhombic 4c-4e o-bond in boron oxide clusters.

PubMed

Tian, Wen-Juan; Zhao, Li-Juan; Chen, Qiang; Ou, Ting; Xu, Hong-Guang; Zheng, Wei-Jun; Zhai, Hua-Jin; Li, Si-Dian

2015-04-07

Gas-phase anion photoelectron spectroscopy (PES) is combined with global structural searches and electronic structure calculations at the hybrid Becke 3-parameter exchange functional and Lee-Yang-Parr correlation functional (B3LYP) and single-point coupled-cluster with single, double, and perturbative triple excitations (CCSD(T)) levels to probe the structural and electronic properties and chemical bonding of the B4O4 (0/-) clusters. The measured PES spectra of B4O4 (-) exhibit a major band with the adiabatic and vertical detachment energies (ADE and VDE) of 2.64 ± 0.10 and 2.81 ± 0.10 eV, respectively, as well as a weak peak with the ADE and VDE of 1.42 ± 0.08 and 1.48 ± 0.08 eV. The former band proves to correspond to the Y-shaped global minimum of Cs B4O4 (-) ((2)A″), with the calculated ADE/VDE of 2.57/2.84 eV at the CCSD(T) level, whereas the weak band is associated with the second lowest-energy, rhombic isomer of D2h B4O4 (-) ((2)B2g) with the predicted ADE/VDE of 1.43/1.49 eV. Both anion structures are planar, featuring a B atom or a B2O2 core bonded with terminal BO and/or BO2 groups. The same Y-shaped and rhombic structures are also located for the B4O4 neutral cluster, albeit with a reversed energy order. Bonding analyses reveal dual three-center four-electron (3c-4e) π hyperbonds in the Y-shaped B4O4 (0/-) clusters and a four-center four-electron (4c-4e) π bond, that is, the so-called o-bond in the rhombic B4O4 (0/-) clusters. This work is the first experimental study on a molecular system with an o-bond.

Electronic Structure of a Self-Assembled Monolayer with Two Surface Anchors: 6-Mercaptopurine on Au(111).

PubMed

Fernández, Cynthia C; Pensa, Evangelina; Carro, Pilar; Salvarezza, Roberto; Williams, Federico J

2018-05-22

The electronic structure of aromatic and aliphatic thiols on Au(111) has been extensively studied in relation to possible applications in molecular electronics. In this work, the effect on the electronic structure of an additional anchor to the S-Au bond using 6-mercaptopurine as a model system has been investigated. Results from X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure spectroscopy, and density functional theory (DFT) confirm that this molecule adsorbs on Au(111) with S-Au and iminic N-Au bonds. Combined ultraviolet photoelectron spectroscopy and DFT data reveal that formation of the 6MP self-assembled monolayer generates a molecular dipole perpendicular to the surface, with negative charges residing at the metal/monolayer interface and positive charges at the monolayer/vacuum interface, which lowers the substrate work function. Scanning tunneling microscopy shows two surface molecular domains: a well-ordered rectangular lattice where molecules are tilted on average 30° with respect to the substrate and aligned 6MP islands where molecules are standing upright. Finally, we found a new electronic state located at -1.7 eV with respect to the Fermi level that corresponds to a localized π molecular state, while the state corresponding to the N-Au bond is hybridized with Au d electrons and stabilized at much lower energies (-3 eV).

Prediction of the electron redundant SinNn fullerenes

NASA Astrophysics Data System (ADS)

Yang, Huihui; Song, Yan; Zhang, Yan; Chen, Hongshan

2018-05-01

The stabilities and electronic structures of SimAln-mNn and SinNn (n = 16, 20, m = 12 and n = 24, m = 16) fullerene-like cages have been investigated using density functional method B3LYP and the second-order perturbation theory MP2. The results show that the SimAln-mNn and SinNn fullerenes are more stable than the AlN counterparts. Comparing with the corresponding AlnNn cages, one silicon atom in each Si2N2 square protrudes and the excess electrons reside as lone pair electrons at the outside of the protrudent Si atoms. Analyses on the electronic structures suggest that the Sisbnd N bonds are covalent bonding with strong polarity. The ELF (electron localization function) shows large electron pair probability between Si and N atoms. The orbital interactions between Si and N are stronger than that between Al and N atoms; the overlap integral is 0.40 per Sisbnd N bond in SinNn and 0.34 per Alsbnd N bond in AlnNn. The AIM (atoms in molecule) charges on the Al atoms in AlnNn and SimAln-mNn are 2.37 and 2.40. The charges on the in-plane and protrudent Si atoms are about 2.88 and 1.50 respectively. Considering the large local dipole moments around the protrudent Si atoms, the electrostatic interactions are also favorable to the SiN cages.

Peculiarities of electron density distribution in bismuth chalcogenides, iron pnictides, cuprates and related unconventional superconductors

NASA Astrophysics Data System (ADS)

Orlov, V. G.; Sergeev, G. S.

2018-05-01

With the aim to reveal the origin of instabilities in the electron subsystem of unconventional superconductors, such as stripes or nematic symmetry breaking, electron band structure calculations were performed for a number of bismuth chalcogenides, bismuth oxide, iron pnictides, as well as for Bi2Sr2CaCu2O8, YBa2Cu3O7 and La2CuO4. It was found that bond critical points in the electron density distribution ρ(r) of all the studied compounds were characterized by positive sign of electron density Laplacian evidencing on depletion of electron charge from the area of bond critical points. A correlation was found between the Tc and the value of electron density Laplacian in the strongest bond critical points of superconductors and related substances.

Selectivity of peptide bond dissociation on excitation of a core electron: Effects of a phenyl group

NASA Astrophysics Data System (ADS)

Tsai, Cheng-Cheng; Chen, Jien-Lian; Hu, Wei-Ping; Lin, Yi-Shiue; Lin, Huei-Ru; Lee, Tsai-Yun; Lee, Yuan T.; Ni, Chi-Kung; Liu, Chen-Lin

2016-09-01

The selective dissociation of a peptide bond upon excitation of a core electron in acetanilide and N-benzylacetamide was investigated. The total-ion-yield near-edge X-ray absorption fine structure spectra were recorded and compared with the predictions from time-dependent density functional theory. The branching ratios for the dissociation of a peptide bond are observed as 16-34% which is quite significant. This study explores the core-excitation, the X-ray photodissociation pathways, and the theoretical explanation of the NEXAFS spectra of organic molecules containing both a peptide bond and a phenyl group.

Geometric, electronic, and bonding properties of AuNM (N = 1-7, M = Ni, Pd, Pt) clusters.

PubMed

Yuan, D W; Wang, Yang; Zeng, Zhi

2005-03-15

Employing first-principles methods, based on density functional theory, we report the ground state geometric and electronic structures of gold clusters doped with platinum group atoms, Au(N)M (N = 1-7, M = Ni, Pd, Pt). The stability and electronic properties of Ni-doped gold clusters are similar to that of pure gold clusters with an enhancement of bond strength. Due to the strong d-d or s-d interplay between impurities and gold atoms originating in the relativistic effects and unique properties of dopant delocalized s-electrons in Pd- and Pt-doped gold clusters, the dopant atoms markedly change the geometric and electronic properties of gold clusters, and stronger bond energies are found in Pt-doped clusters. The Mulliken populations analysis of impurities and detailed decompositions of bond energies as well as a variety of density of states of the most stable dopant gold clusters are given to understand the different effects of individual dopant atom on bonding and electronic properties of dopant gold clusters. From the electronic properties of dopant gold clusters, the different chemical reactivity toward O(2), CO, or NO molecule is predicted in transition metal-doped gold clusters compared to pure gold clusters.

First principle investigation of electronic structure, chemical bonding and optical properties of tetrabarium gallium trinitride oxide single crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khan, Saleem Ayaz, E-mail: sayaz_usb@yahoo.com; Azam, Sikander

The electronic band structure, valence electron charge density and optical susceptibilities of tetrabarium gallium trinitride (TGT) were calculated via first principle study. The electronic band structure calculation describes TGT as semiconductor having direct band gap of 1.38 eV. The valence electronic charge density contour verified the non-polar covalent nature of the bond. The absorption edge and first peak of dielectric tensor components showed electrons transition from N-p state to Ba-d state. The calculated uniaxial anisotropy (0.4842) and birefringence (−0.0061) of present paper is prearranged as follow the spectral components of the dielectric tensor. The first peak in energy loss functionmore » (ELOS) shows the energy loss of fast traveling electrons in the material. The first sharp peak produced in ELOS around 10.5 eV show plasmon loss having plasma frequencies 0.1536, 0.004 and 0.066 of dielectric tensor components. This plasmon loss also cause decrease in reflectivity spectra.« less

Vacuum ultraviolet spectroscopy of the lowest-lying electronic state in subcritical and supercritical water

NASA Astrophysics Data System (ADS)

Marin, Timothy W.; Janik, Ireneusz; Bartels, David M.; Chipman, Daniel M.

2017-05-01

The nature and extent of hydrogen bonding in water has been scrutinized for decades, including how it manifests in optical properties. Here we report vacuum ultraviolet absorption spectra for the lowest-lying electronic state of subcritical and supercritical water. For subcritical water, the spectrum redshifts considerably with increasing temperature, demonstrating the gradual breakdown of the hydrogen-bond network. Tuning the density at 381 °C gives insight into the extent of hydrogen bonding in supercritical water. The known gas-phase spectrum, including its vibronic structure, is duplicated in the low-density limit. With increasing density, the spectrum blueshifts and the vibronic structure is quenched as the water monomer becomes electronically perturbed. Fits to the supercritical water spectra demonstrate consistency with dimer/trimer fractions calculated from the water virial equation of state and equilibrium constants. Using the known water dimer interaction potential, we estimate the critical distance between molecules (ca. 4.5 Å) needed to explain the vibronic structure quenching.

Vacuum ultraviolet spectroscopy of the lowest-lying electronic state in subcritical and supercritical water

DOE PAGES

Marin, Timothy W.; Janik, Ireneusz; Bartels, David M.; ...

2017-05-17

The nature and extent of hydrogen bonding in water has been scrutinized for decades, including how it manifests in optical properties. Here we report vacuum ultraviolet absorption spectra for the lowest-lying electronic state of subcritical and supercritical water. For subcritical water, the spectrum redshifts considerably with increasing temperature, demonstrating the gradual breakdown of the hydrogen-bond network. Tuning the density at 381°C gives insight into the extent of hydrogen bonding in supercritical water. The known gas-phase spectrum, including its vibronic structure, is duplicated in the low-density limit. With increasing density, the spectrum blueshifts and the vibronic structure is quenched as themore » water monomer becomes electronically perturbed. Fits to the supercritical water spectra demonstrate consistency with dimer/trimer fractions calculated from the water virial equation of state and equilibrium constants. As a result, using the known water dimer interaction potential, we estimate the critical distance between molecules (ca. 4.5 Å) needed to explain the vibronic structure quenching.« less

Bulk and surface structural investigations of diesel engine soot and carbon black.

PubMed

Müller, J-O; Su, D S; Wild, U; Schlögl, R

2007-08-14

The microstructure and electronic structure of environmentally relevant carbons such as Euro IV heavy duty diesel engine soot, soot from a black smoking diesel engine, spark discharge soot as model aerosol, commercial furnace soot and lamp black are investigated by transmission electron microscopy, electron energy-loss spectroscopy and X-ray photoelectron spectroscopy. The materials exhibit differences in the predominant bonding, which influences microstructure as well as surface functionalization. These chemical and physical properties depend on the formation history of the investigated carbonaceous materials. In this work, a correlation of the microstructure of the samples to the predominant bonding and incorporation of oxygen into the carbons is obtained. It is shown that a high amount of defects and the deviation of the carbons from a perfect graphitic structure results in a increased incorporation of oxygen and hydrogen. A correlation between the length and curvature of graphene layers with the bonding state of carbon atoms and incorporation of oxygen and hydrogen is established.

On the transferability of electron density in binary vanadium borides VB, V3B4 and VB2.

PubMed

Terlan, Bürgehan; Akselrud, Lev; Baranov, Alexey I; Borrmann, Horst; Grin, Yuri

2015-12-01

Binary vanadium borides are suitable model systems for a systematic analysis of the transferability concept in intermetallic compounds due to chemical intergrowth in their crystal structures. In order to underline this structural relationship, topological properties of the electron density in VB, V3B4 and VB2 reconstructed from high-resolution single-crystal X-ray diffraction data as well as derived from quantum chemical calculations, are analysed in terms of Bader's Quantum Theory of Atoms in Molecules [Bader (1990). Atoms in Molecules: A Quantum Theory, 1st ed. Oxford: Clarendon Press]. The compounds VB, V3B4 and VB2 are characterized by a charge transfer from the metal to boron together with two predominant atomic interactions, the shared covalent B-B interactions and the polar covalent B-M interactions. The resembling features of the crystal structures are well reflected by the respective B-B interatomic distances as well as by ρ(r) values at the B-B bond critical points. The latter decrease with an increase in the corresponding interatomic distances. The B-B bonds show transferable electron density properties at bond critical points depending on the respective bond distances.

High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics

PubMed Central

Kuster, Daniel J.; Liu, Chengyu; Fang, Zheng; Ponder, Jay W.; Marshall, Garland R.

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.613 α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding. PMID:25894612

High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

PubMed

Kuster, Daniel J; Liu, Chengyu; Fang, Zheng; Ponder, Jay W; Marshall, Garland R

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.6(13) α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.6(13/10)-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding.

Phase stability and electronic structure of UMo2Al20: A first-principles study

NASA Astrophysics Data System (ADS)

Liu, Peng-Chuang; Xian, Ya-Jiang; Wang, Xin; Zhang, Yu-Ting; Zhang, Peng-Cheng

2017-09-01

In this paper, the phase stability of UMo2Al20 was explored using cluster formula in combination with first-principles calculations. Cluster formula analysis uncovered that the compound was composed of two principal clusters, i.e. [Mo-Al12] and [U-Al16]. The electronic interactions between U, Mo and Al atoms in this compound were discussed using elastic property, Bader charges and energy-resolved local bonding analysis, as well as the electronic interactions between Mo and Al atoms in [Mo-Al12] cluster and between U and Al atoms in [U-Al16] cluster. It revealed that UMo2Al20 satisfied the mechanical stability criterion for cubic system, and exhibited near ionic bonding character with weak bonding directionality. The calculations within both standard DFT and HSE frameworks demonstrated that U and Al atoms acted as an electron donor while Mo atoms acted as electron acceptor. The intrinsic stability of UMo2Al20 mainly stemmed from the bonding states of Mo-Al bonds and Al-Al bonds in [Mo-Al12] cluster. These calculations provide a further insight on the CeCr2Al20-type ternary compounds.

The Existence of a Designer Al=Al Double Bond in the LiAl2 H4- Cluster Formed by Electronic Transmutation.

PubMed

Lundell, Katie A; Zhang, Xinxing; Boldyrev, Alexander I; Bowen, Kit H

2017-12-22

The Al=Al double bond is elusive in chemistry. Herein we report the results obtained via combined photoelectron spectroscopy and ab initio studies of the LiAl 2 H 4 - cluster that confirm the formation of a conventional Al=Al double bond. Comprehensive searches for the most stable structures of the LiAl 2 H 4 - cluster have shown that the global minimum isomer I possesses a geometric structure which resembles that of Si 2 H 4 , demonstrating a successful example of the transmutation of Al atoms into Si atoms by electron donation. Theoretical simulations of the photoelectron spectrum discovered the coexistence of two isomers in the ion beam, including the one with the Al=Al double bond. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Precise Nanoelectronics with Adatom Chains

NASA Technical Reports Server (NTRS)

Yamada, Toshishige

1999-01-01

Adatom chains on an atomically regulated substrate will be building components in future precise nanoelectronics. Adatoms need to be secured with chemical bonding, but then electronic isolation between the adatom and substrate systems is not guaranteed. A one-dimensional model shows that good isolation with existence of surface states is expected on an s-p crossing substrate such as Si, Ge, or GaAs, reflecting the bulk nature of the substrate. Isolation is better if adatoms are electronically similar to the substrate atoms, and can be manipulated by hydrogenation. Chain structures with group IV adatoms with two chemical bonds, or group III adatoms with one chemical bond, are semiconducting, reflecting the surface nature of the substrate. These structures are unintentionally doped due to the charge transfer across the chemical bonds. Physical properties of adatom chains have to be determined for the unified adatom-substrate system.

Computational study of the process of hydrogen bond breaking: the case of the formamide-formic acid complex.

PubMed

Pacios, Luis F

2006-11-15

MP2/6-311++G(d,p) and B3LYP/6-311++G(d,p) quantum calculations are used to study the formamide-formic acid complex (FFAC), a system bound by two hydrogen bonds, N--H...O and O--H...O, that forms a bond ring at equilibrium. When the intermolecular separation between monomers R increases, this ring opens at a distance for which the weaker N--H...O bond breaks remaining the stronger O--H...O bond. The computational study characterizes that process addressing changes of interaction energy DeltaE, structure and properties of the electron density rho(r) as well as spatial distributions of rho(r), the electrostatic potential U(r), and the electron localization function eta(r). It is shown that the spatial derivatives of DeltaE, the topology of rho(r), and qualitative changes noticed in U(r) = 0 isocontours allow to identify a precise distance R for which one can say the N--H...O hydrogen bond has broken. Both levels of theory predict essentially the same changes of structure and electron properties associated to the process of breaking and virtually identical distances at which it takes place. (c) 2006 Wiley Periodicals, Inc. J Comput Chem, 2006.

Atomic scale structure and chemistry of interfaces by Z-contrast imaging and electron energy loss spectroscopy in the stem

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGibbon, M.M.; Browning, N.D.; Chisholm, M.F.

The macroscopic properties of many materials are controlled by the structure and chemistry at grain boundaries. A basic understanding of the structure-property relationship requires a technique which probes both composition and chemical bonding on an atomic scale. High-resolution Z-contrast imaging in the scanning transmission electron microscope (STEM) forms an incoherent image in which changes in atomic structure and composition across an interface can be interpreted directly without the need for preconceived atomic structure models. Since the Z-contrast image is formed by electrons scattered through high angles, parallel detection electron energy loss spectroscopy (PEELS) can be used simultaneously to provide complementarymore » chemical information on an atomic scale. The fine structure in the PEEL spectra can be used to investigate the local electronic structure and the nature of the bonding across the interface. In this paper we use the complimentary techniques of high resolution Z-contrast imaging and PEELS to investigate the atomic structure and chemistry of a 25{degree} symmetric tilt boundary in a bicrystal of the electroceramic SrTiO{sub 3}.« less

Theoretical study for pyridinium-based ionic liquid 1-ethylpyridinium trifluoroacetate: synthesis mechanism, electronic structure, and catalytic reactivity.

PubMed

Zhu, Xueying; Cui, Peng; Zhang, Dongju; Liu, Chengbu

2011-07-28

By performing density functional theory calculations, we have studied the synthesis mechanism, electronic structure, and catalytic reactivity of a pyridinium-based ionic liquid, 1-ethylpyridinium trifluoroacetate ([epy](+)[CF(3)COO](-)). It is found that the synthesis of the pyridinium salt follows a S(N)2 mechanism. The electronic structural analyses show that multiple H bonds are generally involved in the pyridinium-based ionic liquid, which may play a decisive role for stabilizing the ionic liquid. The cation-anion interaction mainly involves electron transfer between the lone pair of the oxygen atom in the anion and the antibonding orbital of the C*-H bond (C* denotes the carbon atom at the ortho-position of nitrogen atom in the cation). This present work has also given clearly the catalytic mechanism of [epy](+)[CF(3)COO](-) toward to the Diels-Alder (D-A) reaction of acrylonitrile with 2-methyl-1,3-butadiene. Both the cation and anion are shown to play important roles in promoting the D-A reaction. The cation [epy](+), as a Lewis acid, associates the C≡N group by C≡N···H H bond to increase the polarity of the C═C double bond in acrylonitrile, while the anion CF(3)COO(-) links with the methyl group in 2-methyl-1,3-butadiene by C-H···O H bond, which weakens the electron-donating capability of methyl and thereby lowers the energy barrier of the D-A reaction. The present results are expected to provide valuable information for the design and application of pyridinium-based ionic liquids. © 2011 American Chemical Society

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lawler, Keith V.; Childs, Bradley C.; Mast, Daniel S.

The molecular and electronic structures for the Group 7b heptoxides were investigated by computational methods as both isolated molecules and in the solid-state. The metal-oxygen-metal bending angle of the single molecule increased with increasing atomic number, with Re 2O 7 preferring a linear structure. Natural bond orbital and localized orbital bonding analyses indicate that there is a three-center covalent bond between the metal atoms and the bridging oxygen, and the increasing ionic character of the bonds favors larger bond angles. The calculations accurately reproduce the experimental crystal structures within a few percent. Analysis of the band structures and density ofmore » states shows similar bonding for all of the solid-state heptoxides, including the presence of the three-center covalent bond. DFT+U simulations show that PBE-D3 underpredicts the band gap by ~0.2 eV due to an under-correlation of the metal d conducting states. As a result, homologue and compression studies show that Re 2O 7 adopts a polymeric structure because the Re-oxide tetrahedra are easily distorted by packing stresses to form additional three-center covalent bonds.« less

The Nature of Bonding in Bulk Tellurium Composed of One-Dimensional Helical Chains.

PubMed

Yi, Seho; Zhu, Zhili; Cai, Xiaolin; Jia, Yu; Cho, Jun-Hyung

2018-05-07

Bulk tellurium (Te) is composed of one-dimensional (1D) helical chains which have been considered to be coupled by van der Waals (vdW) interactions. However, on the basis of first-principles density functional theory calculations, we here propose a different bonding nature between neighboring chains: i.e., helical chains made of normal covalent bonds are connected together by coordinate covalent bonds. It is revealed that the lone pairs of electrons of Te atoms participate in forming coordinate covalent bonds between neighboring chains, where each Te atom behaves as both an electron donor to neighboring chains and an electron acceptor from neighboring chains. This ligand-metal-like bonding nature in bulk Te results in the same order of bulk moduli along the directions parallel and perpendicular to the chains, contrasting with the large anisotropy of bulk moduli in vdW crystals. We further find that the electron effective masses parallel and perpendicular to the chains are almost the same as each other, consistent with the observed nearly isotropic electrical resistivity. It is thus demonstrated that the normal/coordinate covalent bonds parallel/perpendicular to the chains in bulk Te lead to a minor anisotropy in structural and transport properties.

Structural and Functional Characterization of a Cytochrome P450 2B4 F429H Mutant with an Axial Thiolate–Histidine Hydrogen Bond

PubMed Central

2015-01-01

The structural basis of the regulation of microsomal cytochrome P450 (P450) activity was investigated by mutating the highly conserved heme binding motif residue, Phe429, on the proximal side of cytochrome P450 2B4 to a histidine. Spectroscopic, pre-steady-state and steady-state kinetic, thermodynamic, theoretical, and structural studies of the mutant demonstrate that formation of an H-bond between His429 and the unbonded electron pair of the Cys436 axial thiolate significantly alters the properties of the enzyme. The mutant lost >90% of its activity; its redox potential was increased by 87 mV, and the half-life of the oxyferrous mutant was increased ∼37-fold. Single-crystal electronic absorption and resonance Raman spectroscopy demonstrated that the mutant was reduced by a small dose of X-ray photons. The structure revealed that the δN atom of His429 forms an H-bond with the axial Cys436 thiolate whereas the εN atom forms an H-bond with the solvent and the side chain of Gln357. The amide of Gly438 forms the only other H-bond to the tetrahedral thiolate. Theoretical quantification of the histidine–thiolate interaction demonstrates a significant electron withdrawing effect on the heme iron. Comparisons of structures of class I–IV P450s demonstrate that either a phenylalanine or tryptophan is often found at the location corresponding to Phe429. Depending on the structure of the distal pocket heme, the residue at this location may or may not regulate the thermodynamic properties of the P450. Regardless, this residue appears to protect the thiolate from solvent, oxidation, protonations, and other deleterious reactions. PMID:25029089

Relativistic Effects and Gold Site Distributions: Synthesis, Structure, and Bonding in a Polar Intermetallic Na6Cd16Au7

DOE Office of Scientific and Technical Information (OSTI.GOV)

Samal, Saroj L.; Corbett, John D.

Na{sub 6}Cd{sub 16}Au{sub 7} has been synthesized via typical high-temperature reactions, and its structure refined by single crystal X-ray diffraction as cubic, Fm{bar 3}m, a = 13.589(1) {angstrom}, Z = 4. The structure consists of Cd{sub 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{sub 8}(Au2){sub 6/2}(Au1){sub 4/8}], an ordered ternary derivative of Mn{sub 6}Th{sub 23}. Linear muffin-tin-orbital (LMTO)-atomic sphere approximation (ASA) electronic structure calculations indicate that Na{sub 6}Cd{sub 16}Au{sub 7} is metallic and that {approx}76% of the total crystalmore » orbital Hamilton populations (-ICOHP) originate from polar Cd-Au bonding with 18% more from fewer Cd-Cd contacts. Na{sub 6}Cd{sub 16}Au{sub 7} (45 valence electron count (vec)) is isotypic with the older electron-richer Mg{sub 6}Cu{sub 16}Si{sub 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{sup 10} to bonding states without altering the formal vec are the likely origin of these effects.« less

Chemical Bonding of AlH3 Hydride by Al-L2,3 Electron Energy-Loss Spectra and First-Principles Calculations

PubMed Central

Tatsumi, Kazuyoshi; Muto, Shunsuke; Ikeda, Kazutaka; Orimo, Shin-Ichi

2012-01-01

In a previous study, we used transmission electron microscopy and electron energy-loss (EEL) spectroscopy to investigate dehydrogenation of AlH3 particles. In the present study, we systematically examine differences in the chemical bonding states of Al-containing compounds (including AlH3) by comparing their Al-L2,3 EEL spectra. The spectral chemical shift and the fine peak structure of the spectra were consistent with the degree of covalent bonding of Al. This finding will be useful for future nanoscale analysis of AlH3 dehydrogenation toward the cell. PMID:28816996

Electronic structures of WAlO(y) and WAlO(y)(-) (y = 2-4) determined by anion photoelectron spectroscopy and density functional theory calculations.

PubMed

Mann, Jennifer E; Waller, Sarah E; Jarrold, Caroline Chick

2012-07-28

The anion photoelectron spectra of WAlO(y)(-) (y = 2-4) are presented and assigned based on results of density functional theory calculations. The WAlO(2)(-) and WAlO(3)(-) spectra are both broad, with partially resolved vibrational structure. In contrast, the WAlO(4)(-) spectrum features well-resolved vibrational structure with contributions from three modes. There is reasonable agreement between experiment and theory for all oxides, and calculations are in particular validated by the near perfect agreement between the WAlO(4)(-) photoelectron spectrum and a Franck-Condon simulation based on computationally determined spectroscopic parameters. The structures determined from this study suggest strong preferential W-O bond formation, and ionic bonding between Al(+) and WO(y)(-2) for all anions. Neutral species are similarly ionic, with WAlO(2) and WAlO(3) having electronic structure that suggests Al(+) ionically bound to WO(y)(-) and WAlO(4) being described as Al(+2) ionically bound to WO(4)(-2). The doubly-occupied 3sp hybrid orbital localized on the Al center is energetically situated between the bonding O-local molecular orbitals and the anti- or non-bonding W-local molecular orbitals. The structures determined in this study are very similar to structures recently determined for the analogous MoAlO(y)(-)/MoAlO(y) cluster series, with subtle differences found in the electronic structures [S. E. Waller, J. E. Mann, E. Hossain, M. Troyer, and C. C. Jarrold, J. Chem. Phys. 137, 024302 (2012)].

Effect of lattice defects on the electronic structures and floatability of pyrites

NASA Astrophysics Data System (ADS)

Xian, Yong-jun; Wen, Shu-ming; Chen, Xiu-ming; Deng, Jiu-shuai; Liu, Jian

2012-12-01

The electronic structures of three types of lattice defects in pyrites (i.e., As-substituted, Co-substituted, and intercrystalline Au pyrites) were calculated using the density functional theory (DFT). In addition, their band structures, density of states, and difference charge density were studied. The effect of the three types of lattice defects on the pyrite floatability was explored. The calculated results showed that the band-gaps of pyrites with Co-substitution and intercrystalline Au decreased significantly, which favors the oxidation of xanthate to dixanthogen and the adsorption of dixanthogen during pyrite flotation. The stability of the pyrites increased in the following order: As-substituted < perfect < Co-substituted < intercrystalline Au. Therefore, As-substituted pyrite is easier to be depressed by intensive oxidization compared to perfect pyrite in a strongly alkaline medium. However, Co-substituted and intercrystalline Au pyrites are more difficult to be depressed compared to perfect pyrite. The analysis of the Mulliken bond population and the electron density difference indicates that the covalence characteristic of the S-Fe bond is larger compared to the S-S bond in perfect pyrite. In addition, the presence of the three types of lattice defects in the pyrite bulk results in an increase in the covalence level of the S-Fe bond and a decrease in the covalence level of the S-S bond, which affect the natural floatability of the pyrites.

Structural stability, mechanical properties, electronic structures and thermal properties of XS (X = Ti, V, Cr, Mn, Fe, Co, Ni) binary compounds

NASA Astrophysics Data System (ADS)

Liu, Yangzhen; Xing, Jiandong; Fu, Hanguang; Li, Yefei; Sun, Liang; Lv, Zheng

2017-08-01

The properties of sulfides are important in the design of new iron-steel materials. In this study, first-principles calculations were used to estimate the structural stability, mechanical properties, electronic structures and thermal properties of XS (X = Ti, V, Cr, Mn, Fe, Co, Ni) binary compounds. The results reveal that these XS binary compounds are thermodynamically stable, because their formation enthalpy is negative. The elastic constants, Cij, and moduli (B, G, E) were investigated using stress-strain and Voigt-Reuss-Hill approximation, respectively. The sulfide anisotropy was discussed from an anisotropic index and three-dimensional surface contours. The electronic structures reveal that the bonding characteristics of the XS compounds are a mixture of metallic and covalent bonds. Using a quasi-harmonic Debye approximation, the heat capacity at constant pressure and constant volume was estimated. NiS possesses the largest CP and CV of the sulfides.

Crystal growth and electronic structure of low-temperature phase SrMgF{sub 4}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Atuchin, Victor V.; Functional Electronics Laboratory, Tomsk State University, Tomsk 634050; Laboratory of Semiconductor and Dielectric Materials, Novosibirsk State University, Novosibirsk 630090

2016-04-15

Using the vertical Bridgman method, the single crystal of low temperature phase SrMgF{sub 4} is obtained. The crystal is in a very good optical quality with the size of 10×7×5 mm{sup 3}. Detailed photoemission spectra of the element core levels are determined by a monochromatic AlKa (1486.6 eV) X-ray source. Moreover, the first-principles calculations are performed to investigate the electronic structure of SrMgF{sub 4}. A good agreement between experimental and calculated results is achieved. It is demonstrated that almost all the electronic orbitals are strongly localized and the hybridization with the others is very small, but the Mg–F bonds covalencymore » is relatively stronger than that of Sr–F bonds. - Graphical abstract: Large size of low-temperature phase SrMgF{sub 4} crystal was obtained (right) and its electronic structure was investigated by X-ray photoelectron spectroscopy and first-principles calculation (left). - Highlights: • Large size single crystal of low-temperature phase SrMgF{sub 4} is obtained. • Electronic structure of SrMgF{sub 4} is measured by X-ray photoelectron spectroscopy. • Partial densities of states are determined by first-principles calculation. • Good agreement between experimental and calculated results is achieved. • Strong ionic characteristics of chemical bonds are exhibited in SrMgF{sub 4}.« less

Geometric and electronic structures of phenoxyl radicals hydrogen bonded to neutral and cationic partners.

PubMed

Orio, Maylis; Jarjayes, Olivier; Baptiste, Benoit; Philouze, Christian; Duboc, Carole; Mathias, Jenny-Lee; Benisvy, Laurent; Thomas, Fabrice

2012-04-23

Two di-tert-butylphenols incorporating an N-methylbenzimidazole moiety in the ortho or para position have been synthesised ((Me)OH and (pMe)OH, respectively). Their X-ray structures evidence a hydrogen bond between the phenolic proton and the iminic nitrogen atom, whose nature is intra- and intermolecular, respectively. The present studies demonstrate that (Me)OH is readily oxidised by an intramolecular PET mechanism to form the hydrogen-bonded phenoxyl-N-methylbenzimidazolium system ((Me)OH)(.+) , whereas oxidation of (pMe)OH occurs by intermolecular PET, affording the neutral phenoxyl benzimidazole ((pMe)O)(.) system. The deprotonations of (Me)OH and (pMe)OH yield the corresponding phenolate species ((Me)O)(-) and ((pMe)O)(-), respectively, whilst that of the previously reported (H)OH (analogous to (Me)OH but lacking the N-methyl group) produces an unprecedented hydrogen-bonded phenol benzimidazolate species, as evidenced by its X-ray structure. The latter is believed to be in equilibrium in solution with its tautomeric phenolate form, as suggested by NMR, electrochemistry and DFT studies. The one-electron oxidations of the anions occur by a simple ET process affording phenoxyl radical species, whose electronic structure has been studied by HF-EPR spectroscopy and DFT calculations. In particular, analysis of the g(1) tensor shows the order 2.0079>2.0072>2.0069>2.0067 for ((Me)O)(.), ((H)O)(.), ((Me)OH)(.+) and ((H)OH)(.+), respectively. ((Me)O)(.) exhibits the largest g(1) tensor (2.0079), consistent with the absence of intramolecular hydrogen bond. The g(1) tensor of ((H)O)(.) is intermediate between those of ((Me)OH)(.+) and ((Me)O)(.) (g(1)=2.0072), indicating that the phenoxyl oxygen is hydrogen-bonded with a neutral benzimidazole partner. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Local-structure change rendered by electronic localization-delocalization transition in cerium-based metallic glasses

NASA Astrophysics Data System (ADS)

Luo, Qiang; Schwarz, Björn; Swarbrick, Janine C.; Bednarčik, Jozef; Zhu, Yingcai; Tang, Meibo; Zheng, Lirong; Li, Ran; Shen, Jun; Eckert, Jürgen

2018-02-01

With increasing temperature, metallic glasses (MGs) undergo first glass transition without pronounced structural change and then crystallization with distinct variation in structure and properties. The present study shows a structural change of short-range order induced by an electron-delocalization transition, along with an unusual large-volume shrinkage in Ce-based MGs. An f -electron localization-delocalization transition with thermal hysteresis is observed from the temperature dependence of x-ray absorption spectroscopy and resonant inelastic x-ray scattering spectra, indicating an inheritance of the 4 f configuration of pure Ce. However, the delocalization transition becomes broadened due to the local structural heterogeneity and related fluctuation of 4 f levels in the Ce-based MGs. The amorphous structure regulated 4 f delocalization of Ce leads to bond shortening and abnormal structure change of the topological and chemical short-range orders. Due to the hierarchical bonding nature, the structure should change in a similar manner on different length scales (but not isostructurally like the Ce metal) in Ce-based MGs.

An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals

NASA Technical Reports Server (NTRS)

Jackels, C. F.

1985-01-01

Ab initio quantum chemical techniques are used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types are identified. Basis sets of polarized double zeta quality and large scale configuration interaction wave functions are utilized. Based on electronic energies, the covalently bonded HOOOH species is 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen bonded HO---HO2 species has an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen bonded form is planar, possesses one relatively normal hydrogen bond, and has the lowest energy 3A' and 1A' states that are essentially degenerate. The 1A" and 3A" excited states produced by rotation of the unpaired OH electron into the molecular plane are very slightly bound.

High resolution structural characterisation of laser-induced defect clusters inside diamond

NASA Astrophysics Data System (ADS)

Salter, Patrick S.; Booth, Martin J.; Courvoisier, Arnaud; Moran, David A. J.; MacLaren, Donald A.

2017-08-01

Laser writing with ultrashort pulses provides a potential route for the manufacture of three-dimensional wires, waveguides, and defects within diamond. We present a transmission electron microscopy study of the intrinsic structure of the laser modifications and reveal a complex distribution of defects. Electron energy loss spectroscopy indicates that the majority of the irradiated region remains as sp3 bonded diamond. Electrically conductive paths are attributed to the formation of multiple nano-scale, sp2-bonded graphitic wires and a network of strain-relieving micro-cracks.

Electronic structure of transition metal-cysteine complexes from X-ray absorption spectroscopy.

PubMed

Leung, Bonnie O; Jalilehvand, Farideh; Szilagyi, Robert K

2008-04-17

The electronic structures of HgII, NiII, CrIII, and MoV complexes with cysteine were investigated by sulfur K-edge X-ray absorption near-edge structure (XANES) spectroscopy and density functional theory. The covalency in the metal-sulfur bond was determined by analyzing the intensities of the electric-dipole allowed pre-edge features appearing in the XANES spectra below the ionization threshold. Because of the well-defined structures of the selected cysteine complexes, the current work provides a reference set for further sulfur K-edge XAS studies of bioinorganic active sites with transition metal-sulfur bonds from cysteine residues as well as more complex coordination compounds with thiolate ligands.

A theoretical study of molecular structure, optical properties and bond activation of energetic compound FOX-7 under intense electric fields

NASA Astrophysics Data System (ADS)

Tao, Zhiqiang; Wang, Xin; Wei, Yuan; Lv, Li; Wu, Deyin; Yang, Mingli

2017-02-01

Molecular structure, vibrational and electronic absorption spectra, chemical reactivity of energetic compound FOX-7, one of the most widely used explosives, were studied computationally in presence of an electrostatic field of 0.01-0.05 a.u. The Csbnd N bond, which usually triggers the decomposition of FOX-7, is shortened/elongated under a parallel/antiparallel field. The Csbnd N bond activation energy varies with the external electric field, decreasing remarkably with the field strength in regardless of the field direction. This is attributed to two aspects: the bond weakening by the field parallel to the Csbnd N bond and the stabilization effect on the transition-state structure by the field antiparallel to the bond. The variations in the structure and property of FOX-7 under the electric fields were further analyzed with its distributional polarizability, which is dependent on the charge transfer characteristics through the Csbnd N bond.

Electronic Structure and Bonding in Complex Biomolecule

NASA Astrophysics Data System (ADS)

Ouyang, Lizhi

2005-03-01

For over a century vitamin B12 and its enzyme cofactor derivates have persistently attracted research efforts for their vital biological role, unique Co-C bonding, rich red-ox chemistry, and recently their candidacies as drug delivery vehicles etc. However, our understanding of this complex metalorganic molecule's efficient enzyme activated catalytic power is still controversial. We have for the first time calculated the electronic structure, Mulliken effective charge and bonding of a whole Vitamin B12 molecule without any structural simplification by first- principles approaches based on density functional theory using structures determined by high resolution X-ray diffraction. A partial density of states analysis shows excellent agreement with X-ray absorption data and has been used successfully to interpret measured optical absorption spectra. Mulliken bonding analysis of B12 and its derivatives reveal noticeable correlations between the two axial ligands which could be exploited by the enzyme to control the catalytic process. Our calculated X-ray near edge structure of B12 and its derivates using Slater's transition state theory are also in good agreement with experiments. The same approach has been applied to other B12 derivatives, ferrocene peptides, and recently DNA molecules.

Picosecond Pulsed Laser Ablation for the Surface Preparation of Epoxy Composites

NASA Technical Reports Server (NTRS)

Palmieri, Frank; Ledesma, Rodolfo; Fulton, Tayler; Arthur, Alexandria; Eldridge, Keishara; Thibeault, Sheila; Lin, Yi; Wohl, Chris; Connell, John

2017-01-01

As part of a technical challenge under the Advanced Composites Program, methods for improving pre-bond process control for aerospace composite surface treatments and inspections, in conjunction with Federal Aviation Administration guidelines, are under investigation. The overall goal is to demonstrate high fidelity, rapid and reproducible surface treatment and surface characterization methods to reduce uncertainty associated with the bonding process. The desired outcomes are reliable bonded airframe structure, and reduced timeline to certification. In this work, laser ablation was conducted using a q-switched Nd:YVO4 laser capable of nominal pulse durations of 8 picoseconds (ps). Aerospace structural carbon fiber reinforced composites with an epoxy resin matrix were laser treated, characterized, processed into bonded assemblies and mechanically tested. The characterization of ablated surfaces were conducted using scanning electron microscopy (SEM), water contact angle (WCA) goniometry, micro laser induced breakdown spectroscopy (uLIBS), and electron spin resonance (ESR). The bond performance was assessed using a double cantilever beam (DCB) test with an epoxy adhesive. The surface characteristics and bond performance obtained from picosecond ablated carbon fiber reinforced plastics (CFRPs) are presented herein.

Bonding in gold-rare earth [Au2M] (M = Eu, Yb, Lu) ions. A strong covalent gold-lanthanide bond

NASA Astrophysics Data System (ADS)

Páez-Hernández, Dayán; Muñoz-Castro, Alvaro; Arratia-Perez, Ramiro

2017-09-01

The electronic structure and bonding nature of a series of intermetallic gold-lanthanide [Au2Ln] molecules, where Ln = Eu, Yb, Lu is predicted via the DFT and CASSCF/CASPT2 calculations. The 2c-2e bond model shows a good description of the intermetallic bonding which have a large covalent component with important contribution from bonding interaction between the 6s-Au and the 6s-Ln shell of orbitals.

Polymer sol-gel composite inverse opal structures.

PubMed

Zhang, Xiaoran; Blanchard, G J

2015-03-25

We report on the formation of composite inverse opal structures where the matrix used to form the inverse opal contains both silica, formed using sol-gel chemistry, and poly(ethylene glycol), PEG. We find that the morphology of the inverse opal structure depends on both the amount of PEG incorporated into the matrix and its molecular weight. The extent of organization in the inverse opal structure, which is characterized by scanning electron microscopy and optical reflectance data, is mediated by the chemical bonding interactions between the silica and PEG constituents in the hybrid matrix. Both polymer chain terminus Si-O-C bonding and hydrogen bonding between the polymer backbone oxygens and silanol functionalities can contribute, with the polymer mediating the extent to which Si-O-Si bonds can form within the silica regions of the matrix due to hydrogen-bonding interactions.

Structural, electronic and optical properties of well-known primary explosive: Mercury fulminate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yedukondalu, N.; Vaitheeswaran, G., E-mail: gvsp@uohyd.ernet.in

2015-11-28

Mercury Fulminate (MF) is one of the well-known primary explosives since 17th century and it has rendered invaluable service over many years. However, the correct molecular and crystal structures are determined recently after 300 years of its discovery. In the present study, we report pressure dependent structural, elastic, electronic and optical properties of MF. Non-local correction methods have been employed to capture the weak van der Waals interactions in layered and molecular energetic MF. Among the non-local correction methods tested, optB88-vdW method works well for the investigated compound. The obtained equilibrium bulk modulus reveals that MF is softer than themore » well known primary explosives Silver Fulminate (SF), silver azide and lead azide. MF exhibits anisotropic compressibility (b > a > c) under pressure, consequently the corresponding elastic moduli decrease in the following order: C{sub 22} > C{sub 11} > C{sub 33}. The structural and mechanical properties suggest that MF is more sensitive to detonate along c-axis (similar to RDX) due to high compressibility of Hg⋯O non-bonded interactions along that axis. Electronic structure and optical properties were calculated including spin-orbit (SO) interactions using full potential linearized augmented plane wave method within recently developed Tran-Blaha modified Becke-Johnson (TB-mBJ) potential. The calculated TB-mBJ electronic structures of SF and MF show that these compounds are indirect bandgap insulators. Also, SO coupling is found to be more pronounced for 4d and 5d-states of Ag and Hg atoms of SF and MF, respectively. Partial density of states and electron charge density maps were used to describe the nature of chemical bonding. Ag—C bond is more directional than Hg—C bond which makes SF to be more unstable than MF. The effect of SO coupling on optical properties has also been studied and found to be significant for both (SF and MF) of the compounds.« less

Structure of transition-metal cluster compounds: Use of an additional orbital resulting from the f, g character of spd bond orbitals*

PubMed Central

Pauling, Linus

1977-01-01

A general theory of the structure of complexes of the transition metals is developed on the basis of the enneacovalence of the metals and the requirements of the electroneutrality principle. An extra orbital may be provided through the small but not negligible amount of f and g character of spd bond orbitals, and an extra electron or electron pair may be accepted in this orbital for a single metal or a cluster to neutralize the positive electric charge resulting from the partial ionic character of the bonds with ligands, such as the carbonyl group. Examples of cluster compounds of cobalt, ruthenium, rhodium, osmium, and gold are discussed. PMID:16592470

Structure of transition-metal cluster compounds: Use of an additional orbital resulting from the f, g character of spd bond orbitals.

PubMed

Pauling, L

1977-12-01

A general theory of the structure of complexes of the transition metals is developed on the basis of the enneacovalence of the metals and the requirements of the electroneutrality principle. An extra orbital may be provided through the small but not negligible amount of f and g character of spd bond orbitals, and an extra electron or electron pair may be accepted in this orbital for a single metal or a cluster to neutralize the positive electric charge resulting from the partial ionic character of the bonds with ligands, such as the carbonyl group. Examples of cluster compounds of cobalt, ruthenium, rhodium, osmium, and gold are discussed.

Predicting the structural and electronic properties of two-dimensional single layer boron nitride sheets

NASA Astrophysics Data System (ADS)

Li, Xiao-Dong; Cheng, Xin-Lu

2018-02-01

Three two-dimensional (2D) single layer boron nitride sheets have been predicted based on the first-principles calculations. These 2D boron nitride sheets are comprised of equivalent boron atoms and nitride atoms with sp2 and sp bond hybridization. The geometry optimization reflects that they all possess stable planar crystal structures with the space group P 6 bar 2 m (D3h3) symmetry. The charge density distribution manifests that the B-N bonds in these boron nitride sheets are covalent in nature but with ionic characteristics. The tunable band gaps indicate their potential applications in nanoscale electronic and optoelectronic devices by changing the length of sp-bonded Bsbnd N linkages.

Chemical bonding in aqueous hexacyano cobaltate from photon- and electron-detection perspectives

PubMed Central

Lalithambika, Sreeju Sreekantan Nair; Atak, Kaan; Seidel, Robert; Neubauer, Antje; Brandenburg, Tim; Xiao, Jie; Winter, Bernd; Aziz, Emad F.

2017-01-01

The electronic structure of the [Co(CN)6]3− complex dissolved in water is studied using X-ray spectroscopy techniques. By combining electron and photon detection methods from the solutions ionized or excited by soft X-rays we experimentally identify chemical bonding between the metal center and the CN ligand. Non-resonant photoelectron spectroscopy provides solute electron binding energies, and nitrogen 1 s and cobalt 2p resonant core-level photoelectron spectroscopy identifies overlap between metal and ligand orbitals. By probing resonances we are able to qualitatively determine the ligand versus metal character of the respective occupied and non-occupied orbitals, purely by experiment. For the same excitations we also detect the emitted X-rays, yielding the complementary resonant inelastic X-ray scattering spectra. For a quantitative interpretation of the spectra, we perform theoretical electronic-structure calculations. The latter provide both orbital energies and orbital character which are found to be in good agreement with experimental energies and with experimentally inferred orbital mixing. We also report calculated X-ray absorption spectra, which in conjunction with our orbital-structure analysis, enables us to quantify various bonding interactions with a particular focus on the water-solvent – ligand interaction and the strength of π-backbonding between metal and ligand. PMID:28098216

Rich interfacial chemistry and properties of carbon-doped hexagonal boron nitride nanosheets revealed by electronic structure calculations

NASA Astrophysics Data System (ADS)

Xie, Wei; Tamura, Takahiro; Yanase, Takashi; Nagahama, Taro; Shimada, Toshihiro

2018-04-01

The effect of C doping to hexagonal boron nitride (h-BN) to its electronic structure is examined by first principles calculations using the association from π-electron systems of organic molecules embedded in a two-dimensional insulator. In a monolayered carbon-doped structure, odd-number doping with carbon atoms confers metallic properties with different work functions. Various electronic interactions occur between two layers with odd-number carbon substitution. A direct sp3 covalent chemical bond is formed when C replaces adjacent B and N in different layers. A charge transfer complex between layers is found when C replaces B and N in the next-neighboring region, which results in narrower band gaps (e.g., 0.37 eV). Direct bonding between C and B atoms is found when two C atoms in different layers are at a certain distance.

Investigation of electronic structure and chemical bonding of intermetallic Pd2HfIn: An ab-initio study

NASA Astrophysics Data System (ADS)

Bano, Amreen; Gaur, N. K.

2018-05-01

Ab-initio calculations are carried out to study the electronic and chemical bonding properties of Intermetallic full Heusler compound Pd2HfIn which crystallizes in F-43m structure. All calculations are performed by using density functional theory (DFT) based code Quantum Espresso. Generalized gradient approximations (GGA) of Perdew- Burke- Ernzerhof (PBE) have been adopted for exchange-correlation potential. Calculated electronic band structure reveals the metallic character of the compound. From partial density of states (PDoS), we found the presence of relatively high intensity electronic states of 4d-Pd atom at Fermi level. We have found a pseudo-gap just abouve the Fermi level and N(E) at Fermi level is observed to be 0.8 states/eV, these finding indicates the existence of superconducting character in Pd2HfIn.

Enhancement in Organic Photovoltaic Efficiency through the Synergistic Interplay of Molecular Donor Hydrogen Bonding and -Stacking

DOE PAGES

Shewmon, Nathan; Watkins, Davita; Galindo, Johan; ...

2015-07-20

For organic photovoltaic (OPV) cells based on the bulk heterojunction (BHJ) structure, it remains challenging to rationally control the degree of phase separation and percolation within blends of donors and acceptors to secure optimal charge separation and transport. Reported is a bottom-up, supramolecular approach to BHJ OPVs wherein tailored hydrogen bonding (H-bonding) interactions between π-conjugated electron donor molecules encourage formation of vertically aligned donor π-stacks while simultaneously suppressing lateral aggregation; the programmed arrangement facilitates fine mixing with fullerene acceptors and efficient charge transport. The approach is illustrated using conventional linear or branched quaterthiophene donor chromophores outfitted with terminal functional groupsmore » that are either capable or incapable of self-complementary H-bonding. When applied to OPVs, the H-bond capable donors yield a twofold enhancement in power conversion efficiency relative to the comparator systems, with a maximum external quantum efficiency of 64%. H-bond promoted assembly results in redshifted absorption (in neat films and donor:C 60 blends) and enhanced charge collection efficiency despite disparate donor chromophore structure. Both features positively impact photocurrent and fill factor in OPV devices. Film structural characterization by atomic force microscopy, transmission electron microscopy, and grazing incidence wide angle X-ray scattering reveals a synergistic interplay of lateral H-bonding interactions and vertical π-stacking for directing the favorable morphology of the BHJ.« less

Electronic structure calculations on multiply charged anions containing M bond S bonds (M = Cr, Mo, W) and their heterobimetallic cluster complexes

NASA Astrophysics Data System (ADS)

Gili, Pedro; Tsipis, Athanassios C.

Molecular and electronic structures of multiply charged mononuclear [CrS4]2-/3-, [MoOxS4-x]2-/3- (x = 0-4) and [WS4]2-/3- anionic species, and their heterobimetallic dinuclear and trinuclear clusters formulated as [MoOS3(CuCl)]2-, [WOS3(CuCl)]2-, [MoS4{Cu(CN)}]2-, [(CN)Cu(?-CrS4)Cu(CN)]2-, [(CN)Cu(?-MoS4)Cu(CN)]2-, [ClCu(?-MoS4)CuCl]2-, [Cl2Fe(?-MoS4)CuCl2]2-, and [(CN)Cu(?-WS4)Cu(CN)]2- have been investigated using electronic structure calculation (HF, MP4SDQ and DFT) methods. For the discrete mononuclear anions HF/lanl2dz(M)?6-31+G*(S,O) method provided the best description of their molecular structures, while for the heterobimetallic dinuclear and trinuclear clusters the B3LYP/lanl2dz(M)?6-31+G* method gave equilibrium geometries closely resembling the experimental ones. Electronic and spectroscopic (IR, UV-Vis) properties of the thiometalates are discussed in relation to their structures, while the bonding mechanism was analyzed in the framework of the natural bond orbital (NBO) approach. The nature of the highest occupied molecular orbitals (HOMOs) of all thiometalates indicated their ability to act as ligands coordinated with metal centers and forming clusters of higher nuclearity. The lowest-lying vertical one-electron detachment processes from the ground state of the [CrS4]2/3-, [MoOxS4-x]2/3- (x = 0-4) and [WS4]2/3- anions have been calculated using the outer valence Green's function (OVGF) method. Interestingly, in the heterobimetallic dinuclear and trinuclear clusters intemetallic M?M? interactions exist corresponding to d10 ? d0 dative bonding. Finally, the complete energetic and geometric profile of the successive acid-catalyzed formation reactions:and the reverse hydrolysis reactions have been delineated and details of the mechanism have been furnished.

Structural and electronic properties of M-MOF-74 (M = Mg, Co or Mn)

NASA Astrophysics Data System (ADS)

de Oliveira, Aline; de Lima, Guilherme Ferreira; De Abreu, Heitor Avelino

2018-01-01

The Metal-Organic Frameworks M-MOF-74 (M = Mg, Co or Mn) were investigated through Density Functional Theory calculations. Structural parameters and band gap energies were determined in agreement with experimental data, with errors under 2%. The methods Electron Localization Function and Quantum Theory of Atoms in Molecules were applied to the analyses of the electronic density topology of the three solids. These methodologies indicated that the bonds between the metallic cations and the oxygen atoms are predominantly ionic while the other ones are predominantly covalent. Furthermore, non-conventional hydrogen bonds were identified to Mg-MOF-74 and Co-MOF-74, which were not observed to Mn-MOF-74.

Photoelectron spectroscopy of B{sub 4}O{sub 4}{sup −}: Dual 3c-4e π hyperbonds and rhombic 4c-4e o-bond in boron oxide clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Wen-Juan; Chen, Qiang; Ou, Ting

2015-04-07

Gas-phase anion photoelectron spectroscopy (PES) is combined with global structural searches and electronic structure calculations at the hybrid Becke 3-parameter exchange functional and Lee-Yang-Parr correlation functional (B3LYP) and single-point coupled-cluster with single, double, and perturbative triple excitations (CCSD(T)) levels to probe the structural and electronic properties and chemical bonding of the B{sub 4}O{sub 4}{sup 0/−} clusters. The measured PES spectra of B{sub 4}O{sub 4}{sup −} exhibit a major band with the adiabatic and vertical detachment energies (ADE and VDE) of 2.64 ± 0.10 and 2.81 ± 0.10 eV, respectively, as well as a weak peak with the ADE and VDEmore » of 1.42 ± 0.08 and 1.48 ± 0.08 eV. The former band proves to correspond to the Y-shaped global minimum of C{sub s} B{sub 4}O{sub 4}{sup −} ({sup 2}A″), with the calculated ADE/VDE of 2.57/2.84 eV at the CCSD(T) level, whereas the weak band is associated with the second lowest-energy, rhombic isomer of D{sub 2h} B{sub 4}O{sub 4}{sup −} ({sup 2}B{sub 2g}) with the predicted ADE/VDE of 1.43/1.49 eV. Both anion structures are planar, featuring a B atom or a B{sub 2}O{sub 2} core bonded with terminal BO and/or BO{sub 2} groups. The same Y-shaped and rhombic structures are also located for the B{sub 4}O{sub 4} neutral cluster, albeit with a reversed energy order. Bonding analyses reveal dual three-center four-electron (3c-4e) π hyperbonds in the Y-shaped B{sub 4}O{sub 4}{sup 0/−} clusters and a four-center four-electron (4c-4e) π bond, that is, the so-called o-bond in the rhombic B{sub 4}O{sub 4}{sup 0/−} clusters. This work is the first experimental study on a molecular system with an o-bond.« less

Asymmetry and Electronegativity in the Electron Capture Activation of the Se-Se Bond: σ*(Se-Se) vs σ*(Se-X).

PubMed

Gámez, José A; Yáñez, Manuel

2010-10-12

The effects of electron capture on the structure of XSeSeX' diselenide derivatives in which the substituents attached to the selenium atoms have different electronegativities have been investigated at different levels of theory, namely, DFT, MP2, CCSD, G2, and CASSCF/CASPT2. An analysis of the bonding changes upon electron attachment shows that when the diselenides bear low-electronegativity substituents, the Se-Se bond becomes activated upon electron capture, as previous studies have shown. However, this is no longer the case for very electronegative substituents, where this bond remains practically unaltered and is the Se-X bond the one which becomes strongly activated through a preferential population of the σ*(Se-X) antibonding orbital rather than the σ*(Se-Se) one. When this is the case, several anionic species are also encountered, namely, stretched, bent, and book structures. The present findings are similar to those obtained for a series of analogous disulfide compounds, which points out that these results are not unique and could be extrapolated to a wider range of compounds than the ones covered here. The Se-Se (Se-X) linkage in CH3SeSeOH, CH3SeSeF, FSeSeOH, and FSeSeF bears some of the characteristics of the so-called charge-shift bonds, with a clear charge fluctuation between both selenium atoms. This is more evident in their anions where the bonding reflects the important contribution of the ionic resonant forms Se-Se(-) ↔ (-)Se-Se vs the covalent component Se∴Se. This resonance changes with the nature of the substituents but also depends on the asymmetry of the substitution.

Photoelectron spectroscopy of nitromethane anion clusters

NASA Astrophysics Data System (ADS)

Pruitt, Carrie Jo M.; Albury, Rachael M.; Goebbert, Daniel J.

2016-08-01

Nitromethane anion and nitromethane dimer, trimer, and hydrated cluster anions were studied by photoelectron spectroscopy. Vertical detachment energies, estimated electron affinities, and solvation energies were obtained from the photoelectron spectra. Cluster structures were investigated using theoretical calculations. Predicted detachment energies agreed with experiment. Calculations show water binds to nitromethane anion through two hydrogen bonds. The dimer has a non-linear structure with a single ionic Csbnd H⋯O hydrogen bond. The trimer has two different solvent interactions, but both involve the weak Csbnd H⋯O hydrogen bond.

A Comprehensive Analysis in Terms of Molecule-Intrinsic, Quasi-Atomic Orbitals. III. The Covalent Bonding Structure of Urea.

PubMed

West, Aaron C; Schmidt, Michael W; Gordon, Mark S; Ruedenberg, Klaus

2015-10-15

The analysis of molecular electron density matrices in terms of quasi-atomic orbitals, which was developed in previous investigations, is quantitatively exemplified by a detailed application to the urea molecule. The analysis is found to identify strong and weak covalent bonding interactions as well as intramolecular charge transfers. It yields a qualitative as well as quantitative ab initio description of the bonding structure of this molecule, which raises questions regarding some traditional rationalizations.

Secondary Structures in a Freeze-Dried Lignite Humic Acid Fraction Caused by Hydrogen-Bonding of Acidic Protons with Aromatic Rings.

PubMed

Cao, Xiaoyan; Drosos, Marios; Leenheer, Jerry A; Mao, Jingdong

2016-02-16

A lignite humic acid (HA) was separated from inorganic and non-HA impurities (i.e., aluminosilicates, metals) and fractionated by a combination of dialysis and XAD-8 resin. Fractionation revealed a more homogeneous structure of lignite HA. New and more specific structural information on the main lignite HA fraction is obtained by solid-state nuclear magnetic resonance (NMR) spectroscopy. Quantitative (13)C multiple cross-polarization (multiCP) NMR indicated oxidized phenyl propane structures derived from lignin. MultiCP experiments, conducted on potassium HA salts titrated to pH 10 and pH 12, revealed shifts consistent with carboxylate and phenolate formation, but structural changes associated with enolate formation from aromatic beta keto acids were not detected. Two-dimensional (1)H-(13)C heteronuclear correlation (2D HETCOR) NMR indicated aryl-aliphatic ketones, aliphatic and aromatic carboxyl groups, phenol, and methoxy phenyl ethers. Acidic protons from carboxyl groups in both the lignite HA fraction and a synthetic HA-like polycondensate were found to be hydrogen-bonded with electron-rich aromatic rings. Our results coupled with published infrared spectra provide evidence for the preferential hydrogen bonding of acidic hydrogens with electron-rich aromatic rings rather than adjacent carbonyl groups. These hydrogen-bonding interactions likely result from stereochemical arrangements in primary structures and folding.

Quantum chemistry study on the open end of single-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Hou, Shimin; Shen, Ziyong; Zhao, Xingyu; Xue, Zengquan

2003-05-01

Geometrical and electronic structures of open-ended single-walled carbon nanotubes (SWCNTs) are calculated using density functional theory (DFT) with hybrid functional (B3LYP) approximation. Due to different distances between carbon atoms along the edge, reconstruction occurs at the open end of the (4,4) armchair SWCNT, i.e., triple bonds are formed in the carbon atom pairs at the mouth; however, for the (6,0) zigzag SWCNT, electrons in dangling bonds still remain at 'no-bonding' states. The ionization potential (IP) of both (4,4) and (6,0) SWCNTs is increased by their negative intrinsic dipole moments, and localized electronic states existed at both of their open ends.

Theoretical study of structure, bonding, and electronic behavior of novel sandwich compounds M₃(C6R6)₂ (M = Ni, Pd, Pt; R = H, F).

PubMed

Zhou, Ke

2012-10-01

The correlations between the structural and electronic properties of the monolayer clusters M₃ (where M = Ni, Pd, Pt) and the sandwich complexes M₃(C₆R₆)₂ (where M = Ni, Pd, Pt; R = H, F) were studied by performing quantum-chemical calculations. All of the sandwich complexes are strongly donating and backdonating metal-ligand bonding structures. The influence of the ligand as well as significant variations in the M-C, M-M, and C-C bond lengths and binding energies were examined to obtain a qualitative and quantitative picture of the intramolecular interactions in C₆R₆-M₃. Our theoretical investigations show that the binding energies of these sandwich complexes gradually decrease from Ni to Pt as well as from H to F, which can be explained via the frontier orbitals of the clusters M₃ and C₆R₆.

Importance of interlayer H bonding structure to the stability of layered minerals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Conroy, Michele; Soltis, Jennifer A.; Wittman, Rick S.

2017-10-16

The exact atomic structures of layered minerals have been difficult to characterize because the layers often possess out-of-plane hydrogen atoms that cannot be detected by many analytical techniques. However, the ordering of these bonds are thought to play a fundamental role in the structural stability and solubility of layered minerals. We report a new strategy of using the intense radiation field of a focused electron beam to probe the effect of differences in hydrogen bonding networks on mineral solubility while simultaneously imaging the dissolution behavior in real time via liquid cell electron microscopy. We show the loss in hydrogens frommore » interlayers of boehmite (γ-AlOOH) resulted in 2D nanosheets exfoliating from the bulk that subsequently and rapidly dissolved. However gibbsite (γ-Al(OH)3), with its higher concentration of OH terminating groups, was more accommodating to the deprotonation and stable under the beam.« less

Electronic structure and bonding properties of potassium (K) on graphite under external electric field.

NASA Astrophysics Data System (ADS)

Tapia, Alejandro; Canto, Gabriel

2005-03-01

The effect of an external electric field on the potassium (K) adsorption on the graphite surface, are studied by means of first-principles total-energy calculations. The results were obtained with the pseudopotentials LCAO method (SIESTA code) and the Generalized Gradient Approximation (GGA) for the exchange-correlation potential. The structural parameters, bonding properties, and electronic structure of the K-graphite system are studied in the triangular (2x2) overlayer phase as a function of the external electric field magnitude. We find an important change in the K-graphite bonding as a consequence of the charge transfer from the adatom towards the substrate induced by the electric field. The results are discussed in the light of the experimental observed difussion of K into graphite induced by external electric fields. This work was supported by Consejo Nacional de Ciencia y Tecnolog'ia (CONACYT, M'exico) under Grants No. 43830-F and No. 44831-F.

Local Bonding Influence on the Band Edge and Band Gap Formation in Quaternary Chalcopyrites.

PubMed

Miglio, Anna; Heinrich, Christophe P; Tremel, Wolfgang; Hautier, Geoffroy; Zeier, Wolfgang G

2017-09-01

Quaternary chalcopyrites have shown to exhibit tunable band gaps with changing anion composition. Inspired by these observations, the underlying structural and electronic considerations are investigated using a combination of experimentally obtained structural data, molecular orbital considerations, and density functional theory. Within the solid solution Cu 2 ZnGeS 4- x Se x , the anion bond alteration parameter changes, showing larger bond lengths for metal-selenium than for metal-sulfur bonds. The changing bonding interaction directly influences the valence and conduction band edges, which result from antibonding Cu-anion and Ge-anion interactions, respectively. The knowledge of the underlying bonding interactions at the band edges can help design properties of these quaternary chalcopyrites for photovoltaic and thermoelectric applications.

Does Compound I Vary Significantly between Isoforms of Cytochrome P450?

PubMed Central

2011-01-01

The cytochrome P450 (CYP) enzymes are important in many areas, including pharmaceutical development. Subtle changes in the electronic structure of the active species, Compound I, have been postulated previously to account partly for the experimentally observed differences in reactivity between isoforms. Current predictive models of CYP metabolism typically assume an identical Compound I in all isoforms. Here we present a method to calculate the electronic structure and to estimate the Fe–O bond enthalpy of Compound I, and apply it to several human and bacterial CYP isoforms. Conformational flexibility is accounted for by sampling large numbers of structures from molecular dynamics simulations, which are subsequently optimized with density functional theory (B3LYP) based quantum mechanics/molecular mechanics. The observed differences in Compound I between human isoforms are small: They are generally smaller than the spread of values obtained for the same isoform starting from different initial structures. Hence, it is unlikely that the variation in activity between human isoforms is due to differences in the electronic structure of Compound I. A larger difference in electronic structure is observed between the human isoforms and P450cam and may be explained by the slightly different hydrogen-bonding environment surrounding the cysteinyl sulfur. The presence of substrate in the active site of all isoforms studied appears to cause a slight decrease in the Fe–O bond enthalpy, apparently due to displacement of water out of the active site, suggesting that Compound I is less stable in the presence of substrate. PMID:21863858

Bond Order and Chemical Properties of BF, CO, and N[subscript 2

ERIC Educational Resources Information Center

Martinie, Ryan J.; Bultema, Jarred J.; Vander Wal, Mark N.; Burkhart, Brandon J.; Vander Griend, Douglas A.; DeKock, Roger L.

2011-01-01

The traditional chemical approaches, Lewis electron dot structures and molecular orbital theory, predict the relative bond orders of boron monofluoride, carbon monoxide, and dinitrogen to be BF less than CO less than N[subscript 2]. This is quantified by quantum mechanical, theoretical studies that show the bond orders to be approximately 1.4,…

Influence of Al grain boundaries segregations and La-doping on embrittlement of intermetallic NiAl

NASA Astrophysics Data System (ADS)

Kovalev, Anatoly I.; Wainstein, Dmitry L.; Rashkovskiy, Alexander Yu.

2015-11-01

The microscopic nature of intergranular fracture of NiAl was experimentally investigated by the set of electron spectroscopy techniques. The paper demonstrates that embrittlement of NiAl intermetallic compound is caused by ordering of atomic structure that leads to formation of structural aluminum segregations at grain boundaries (GB). Such segregations contain high number of brittle covalent interatomic bonds. The alloying by La increases the ductility of material avoiding Al GB enrichment and disordering GB atomic structure. The influence of La alloying on NiAl mechanical properties was investigated. GB chemical composition, atomic and electronic structure transformations after La doping were investigated by AES, XPS and EELFS techniques. To qualify the interatomic bonds metallicity the Fermi level (EF) position and electrons density (neff) in conduction band were determined in both undoped and doped NiAl. Basing on experimental results the physical model of GB brittleness formation was proposed.

XAFS and XEOL of tetramesityldigermene - An electronic structure study of a heavy group 14 ethylene analogue

NASA Astrophysics Data System (ADS)

Ward, Matthew J.; Rupar, Paul A.; Murphy, Michael W.; Yiu, Yun-Mui; Baines, Kim M.; Sham, Tsun-Kong

2013-04-01

Digermene, the germanium analogue of ethylene, has a multiple bonding motif that differs greatly from that of alkenes and exhibits no pure σ or π type bonds. The electronic structure of digermenes is difficult to study experimentally due to their reactivity, and is computationally challenging because of their shallow potential energy surfaces. Using X-ray absorption near edge structures at both the germanium K and L edges we have been able to directly probe the unoccupied electronic states, or the lowest unoccupied molecular orbital (LUMO), and LUMO+ etc. in the Ge=Ge bond of tetramesityldigermene. We have demonstrated that the LUMO, LUMO+, etc. are composed of hybrid Ge 4s and 4p orbitals. Additionally, our data suggest that the LUMO exhibits relatively more Ge 4s character, whereas the LUMO+ and LUMO+2 exhibit relatively more Ge 4p character. An X-ray excited optical luminescence study of Ge2Mes4 revealed one broad optical emission band at 620 nm, which is significantly red shifted compared to the known energy gap of this molecular germanium compound.

Study of Electronic Structure, Thermal Conductivity, Elastic and Optical Properties of α, β, γ-Graphyne

PubMed Central

Hou, Xun; Xie, Zhongjing; Li, Chunmei; Li, Guannan; Chen, Zhiqian

2018-01-01

In recent years, graphyne was found to be the only 2D carbon material that has both sp and sp2 hybridization. It has received significant attention because of its great potential in the field of optoelectronics, which arises due to its small band gap. In this study, the structural stability, electronic structure, elasticity, thermal conductivity and optical properties of α, β, γ-graphynes were investigated using density functional theory (DFT) systematically. γ-graphyne has the largest negative cohesive energy and thus the most stable structure, while the β-graphyne comes 2nd. Both β and γ-graphynes have sp-sp, sp-sp2 and sp2-sp2 hybridization bonds, of which γ-graphyne has shorter bond lengths and thus larger Young’s modulus. Due to the difference in acetylenic bond in the structure cell, the effect of strain on the electronic structure varies between graphynes: α-graphyne has no band gap and is insensitive to strain; β-graphyne’s band gap has a sharp up-turn at 10% strain, while γ-graphyne’s band gap goes up linearly with the strain. All the three graphynes exhibit large free carrier concentration and these free carriers have small effective mass, and both free carrier absorption and intrinsic absorption are found in the light absorption. Based on the effect of strain, optical properties of three structures are also analyzed. It is found that the strain has significant impacts on their optical properties. In summary, band gap, thermal conductivity, elasticity and optical properties of graphyne could all be tailored with adjustment on the amount of acetylenic bonds in the structure cell. PMID:29370070

Study of Electronic Structure, Thermal Conductivity, Elastic and Optical Properties of α, β, γ-Graphyne.

PubMed

Hou, Xun; Xie, Zhongjing; Li, Chunmei; Li, Guannan; Chen, Zhiqian

2018-01-25

In recent years, graphyne was found to be the only 2D carbon material that has both sp and sp² hybridization. It has received significant attention because of its great potential in the field of optoelectronics, which arises due to its small band gap. In this study, the structural stability, electronic structure, elasticity, thermal conductivity and optical properties of α, β, γ-graphynes were investigated using density functional theory (DFT) systematically. γ-graphyne has the largest negative cohesive energy and thus the most stable structure, while the β-graphyne comes 2nd. Both β and γ-graphynes have sp-sp, sp-sp² and sp²-sp² hybridization bonds, of which γ-graphyne has shorter bond lengths and thus larger Young's modulus. Due to the difference in acetylenic bond in the structure cell, the effect of strain on the electronic structure varies between graphynes: α-graphyne has no band gap and is insensitive to strain; β-graphyne's band gap has a sharp up-turn at 10% strain, while γ-graphyne's band gap goes up linearly with the strain. All the three graphynes exhibit large free carrier concentration and these free carriers have small effective mass, and both free carrier absorption and intrinsic absorption are found in the light absorption. Based on the effect of strain, optical properties of three structures are also analyzed. It is found that the strain has significant impacts on their optical properties. In summary, band gap, thermal conductivity, elasticity and optical properties of graphyne could all be tailored with adjustment on the amount of acetylenic bonds in the structure cell.

TEM Analysis of Diffusion-Bonded Silicon Carbide Ceramics Joined Using Metallic Interlayers

NASA Technical Reports Server (NTRS)

Ozaki, T.; Hasegawa, Y.; Tsuda, H.; Mori, S.; Halbig, M. C.; Asthana, R.; Singh, M.

2017-01-01

SiC fiber-bonded ceramics (SA-Tyrannohex: SA-THX) diffusion-bonded with TiCu metallic interlayers were investigated. Thin samples of the ceramics were prepared with a focused ion beam (FIB) and the interfacial microstructure of the prepared samples was studied by transmission electron microscopy (TEM) and scanning TEM (STEM). In addition to conventional microstructure observation, for detailed analysis of reaction compounds in diffusion-bonded area, we performed STEM-EDS measurements and selected area electron diffraction (SAD) experiments. The TEM and STEM experiments revealed the diffusion-bonded area was composed of only one reaction layer, which was characterized by TiC precipitates in Cu-Si compound matrix. This reaction layer was in good contact with the SA-THX substrates, and it is concluded that the joint structure led to the excellent bonding strength.

Alkali metal mediated C-C bond coupling reaction

NASA Astrophysics Data System (ADS)

Tachikawa, Hiroto

2015-02-01

Metal catalyzed carbon-carbon (C-C) bond formation is one of the important reactions in pharmacy and in organic chemistry. In the present study, the electron and hole capture dynamics of a lithium-benzene sandwich complex, expressed by Li(Bz)2, have been investigated by means of direct ab-initio molecular dynamics method. Following the electron capture of Li(Bz)2, the structure of [Li(Bz)2]- was drastically changed: Bz-Bz parallel form was rapidly fluctuated as a function of time, and a new C-C single bond was formed in the C1-C1' position of Bz-Bz interaction system. In the hole capture, the intermolecular vibration between Bz-Bz rings was only enhanced. The mechanism of C-C bond formation in the electron capture was discussed on the basis of theoretical results.

Chemical Ni-C Bonding in Ni-Carbon Nanotube Composite by a Microwave Welding Method and Its Induced High-Frequency Radar Frequency Electromagnetic Wave Absorption.

PubMed

Sha, Linna; Gao, Peng; Wu, Tingting; Chen, Yujin

2017-11-22

In this work, a microwave welding method has been used for the construction of chemical Ni-C bonding at the interface between carbon nanotubes (CNTs) and metal Ni to provide a different surface electron distribution, which determined the electromagnetic (EM) wave absorption properties based on a surface plasmon resonance mechanism. Through a serial of detailed examinations, such as X-ray diffraction, scanning electron microscopy, transmission electron microscopy, high-resolution transmission electron microscopy, X-ray photoelectron spectroscopy, and Raman spectrum, the as-expected chemical Ni-C bonding between CNTs and metal Ni has been confirmed. And the Brunauer-Emmett-Teller and surface zeta potential measurements uncovered the great evolution of structure and electronic density compared with CNTs, metal Ni, and Ni-CNT composite without Ni-C bonding. Correspondingly, except the EM absorption due to CNTs and metal Ni in the composite, another wide and strong EM absorption band ranging from 10 to 18 GHz was found, which was induced by the Ni-C bonded interface. With a thinner thickness and more exposed Ni-C interfaces, the Ni-CNT composite displayed less reflection loss.

Understanding molecular structure from molecular mechanics.

PubMed

Allinger, Norman L

2011-04-01

Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

Theoretical studies of damage to 3'-uridine monophosphate induced by electron attachment.

PubMed

Zhang, Ru Bo; Zhang, Ke; Eriksson, Leif A

2008-01-01

Low-energy electrons (LEE) are well known to induce nucleic acid damage. However, the damage mechanisms related to charge state and structural features remain to be explored in detail. In the present work, we have investigated the N1-glycosidic and C3'-O(P) bond ruptures of 3'-UMP (UMP=uridine monophosphate) and the protonated form 3'-UMPH with -1 and zero charge, respectively, based on hybrid density functional theory (DFT) B3 LYP together with the 6-31+G(d,p) basis set. The glycosidic bond breakage reactions of the 3'UMP and 3'UMPH electron adducts are exothermic in both cases, with barrier heights of 19-20 kcal mol(-1) upon inclusion of bulk solvation. The effects of the charge state on the phosphate group are marginal, but the C2'-OH group destabilizes the transition structure of glycosidic bond rupture of 3'-UMPH in the gas phase by approximately 5.0 kcal mol(-1). This is in contrast with the C3'-O(P) bond ruptures induced by LEE in which the charge state on the phosphate influences the barrier heights and reaction energies considerably. The barrier towards C3'-O(P) bond dissociation in the 3'UMP electron adduct is higher in the gas phase than the one corresponding to glycosidic bond rupture and is dramatically influenced by the C2'-OH group and bulk salvation, which decreases the barrier to 14.7 kcal mol(-1). For the C3'-O(P) bond rupture of the 3'UMPH electron adduct, the reaction is exothermic and the barrier is even lower, 8.2 kcal mol(-1), which is in agreement with recent results for 3'-dTMPH and 5'-dTMPH (dTMPH=deoxythymidine monophosphate). Both the Mulliken atomic charges and unpaired-spin distribution play significant roles in the reactions.

Spin Uncoupling in Chemisorbed OCCO and CO 2: Two High-Energy Intermediates in Catalytic CO 2 Reduction

DOE PAGES

Hedstrom, Svante; dos Santos, Egon Campos; Liu, Chang; ...

2018-05-08

Here, the production of useful compounds via the electrochemical carbon dioxide reduction reaction (CO2RR) is a matter of intense research. Although the thermodynamics and kinetic barriers of CO2RR are reported in previous computational studies, the electronic structure details are often overlooked. We study two important CO2RR intermediates: ethylenedione (OCCO) and CO 2 covalently bound to cluster and slab models of the Cu(100) surface. Both molecules exhibit a near-unity negative charge as chemisorbed, but otherwise they behave quite differently, as explained by a spin-uncoupling perspective. OCCO adopts a high-spin, quartetlike geometry, allowing two covalent bonds to the surface with an averagemore » gross interaction energy of –1.82 eV/bond. The energy cost for electronically exciting OCCO– to the quartet state is 1.5 eV which is readily repaid via the formation of its two surface bonds. CO 2, conversely, retains a low-spin, doubletlike structure upon chemisorption, and its single unpaired electron forms a single covalent surface bond of –2.07 eV. The 5.0 eV excitation energy to the CO 2 – quartet state is prohibitively costly and cannot be compensated for by an additional surface bond.« less

Ab initio study of properties of BaBiO3 at high pressure

NASA Astrophysics Data System (ADS)

Martoňák, Roman; Ceresoli, Davide; Kagayama, Tomoko; Tosatti, Erio

BaBiO3 is a mixed-valence perovskite which escapes metallic state by creating a Bi-O bond disproportionation or CDW pattern, resulting in a Peierls semiconductor with gap of nearly 1 eV at zero pressure. Evolution of structural and electronic properties at high pressure is, however, largely unknown. Pressure, it might be natural to expect, could reduce the bond-disproportionation and bring the system closer to metalicity or even superconductivity. We address this question by ab initio DFT methods based on GGA and hybrid functionals in combination with crystal structure prediction techniques based on genetic algorithms. We analyze the pressure evolution of bond disproportionation as well as other order parameters related to octahedra rotation for various phases in connection with corresponding evolution of the electronic structure. Results indicate that BaBiO3 continues to resist metalization also under pressure, through structural phase transitions which sustain and in fact increase the diversity of length of Bi-O bonds for neighboring Bi ions, in agreement with preliminary high pressure resistivity data. R.M. Slovak Research and Development Agency Contract APVV-15-0496, VEGA project No. 1-0904-15; E.T. ERC MODPHYSFRICT Advanced Grant No. 320796.

To bend or not to bend: electronic structural analysis of linear versus bent M-H-M interactions in dinickel bis(dialkylphosphino)methane complexes.

PubMed

Wilson, Zakiya S; Stanley, George G; Vicic, David A

2010-06-21

The M-H-M bonding in the dinuclear complexes Ni(2)(mu-H)(mu-P(2))(2)X(2) (P(2) = R(2)PCH(2)PR(2), R = iPr, Cy; X = Cl, Br) has been investigated. These dinickel A-frames were studied via density functional theory (DFT) calculations to analyze the factors that influence linear and bent M-H-M bonding. The DFT calculations indicate that the bent geometry is favored electronically, with ligand steric effects driving the formation of the linear M-H-M structures.

Electronic Structure of Actinides under Pressure

NASA Astrophysics Data System (ADS)

Johansson, Borje

2006-03-01

The series of heavy radioactive elements known as the actinides all have similar elemental properties. However, when the volume per atom in the condensed phase is illustrated as a function of atomic number, perhaps the most dramatic anomaly in the periodic table becomes apparent. The atomic volume of americium is almost 50% larger than it is for the preceding element plutonium. For the element after americium, curium, the atomic volume is very close to that of americium. The same holds also for the next elements berkelium and californium. Accordingly from americium and onwards the actinides behave very similar to the corresponding rare-earth elements - a second lanthanide series of metallic elements can be identified. This view is strongly supported by the fact that all these elements adopt the dhcp structure, a structure typical for the lanthanides. The reason for this behavior is found in the behavior of the 5f electrons. For the earlier actinides, up to and including plutonium, the 5f electrons form metallic states and contribute most significantly to the bonding. In Np and Pu they even dominate the bonding, while all of a sudden they become localized in Am, very much like the 4f electrons in the lanthanide series, and contribute no longer to the cohesion. This withdrawal of 5f bonding gives rise to the large volume expansion between plutonium and americium. This difference between the light and heavy actinide suggests that it would be most worthwhile to strongly compress the transplutonium elements, thereby forcing the individual 5f electron wave functions into strong contact with each other (overlap). Recently high pressure experiments have been performed for americium and curium and dramatic crystal structure changes have been observed. These results and other high pressure data will be discussed in relation to the basic electronic structure of these elements.

Disorder and defects are not intrinsic to boron carbide

NASA Astrophysics Data System (ADS)

Mondal, Swastik; Bykova, Elena; Dey, Somnath; Ali, Sk Imran; Dubrovinskaia, Natalia; Dubrovinsky, Leonid; Parakhonskiy, Gleb; van Smaalen, Sander

2016-01-01

A unique combination of useful properties in boron-carbide, such as extreme hardness, excellent fracture toughness, a low density, a high melting point, thermoelectricity, semi-conducting behavior, catalytic activity and a remarkably good chemical stability, makes it an ideal material for a wide range of technological applications. Explaining these properties in terms of chemical bonding has remained a major challenge in boron chemistry. Here we report the synthesis of fully ordered, stoichiometric boron-carbide B13C2 by high-pressure-high-temperature techniques. Our experimental electron-density study using high-resolution single-crystal synchrotron X-ray diffraction data conclusively demonstrates that disorder and defects are not intrinsic to boron carbide, contrary to what was hitherto supposed. A detailed analysis of the electron density distribution reveals charge transfer between structural units in B13C2 and a new type of electron-deficient bond with formally unpaired electrons on the C-B-C group in B13C2. Unprecedented bonding features contribute to the fundamental chemistry and materials science of boron compounds that is of great interest for understanding structure-property relationships and development of novel functional materials.

Understanding boron through size-selected clusters: structure, chemical bonding, and fluxionality.

PubMed

Sergeeva, Alina P; Popov, Ivan A; Piazza, Zachary A; Li, Wei-Li; Romanescu, Constantin; Wang, Lai-Sheng; Boldyrev, Alexander I

2014-04-15

Boron is an interesting element with unusual polymorphism. While three-dimensional (3D) structural motifs are prevalent in bulk boron, atomic boron clusters are found to have planar or quasi-planar structures, stabilized by localized two-center-two-electron (2c-2e) σ bonds on the periphery and delocalized multicenter-two-electron (nc-2e) bonds in both σ and π frameworks. Electron delocalization is a result of boron's electron deficiency and leads to fluxional behavior, which has been observed in B13(+) and B19(-). A unique capability of the in-plane rotation of the inner atoms against the periphery of the cluster in a chosen direction by employing circularly polarized infrared radiation has been suggested. Such fluxional behaviors in boron clusters are interesting and have been proposed as molecular Wankel motors. The concepts of aromaticity and antiaromaticity have been extended beyond organic chemistry to planar boron clusters. The validity of these concepts in understanding the electronic structures of boron clusters is evident in the striking similarities of the π-systems of planar boron clusters to those of polycyclic aromatic hydrocarbons, such as benzene, naphthalene, coronene, anthracene, or phenanthrene. Chemical bonding models developed for boron clusters not only allowed the rationalization of the stability of boron clusters but also lead to the design of novel metal-centered boron wheels with a record-setting planar coordination number of 10. The unprecedented highly coordinated borometallic molecular wheels provide insights into the interactions between transition metals and boron and expand the frontier of boron chemistry. Another interesting feature discovered through cluster studies is boron transmutation. Even though it is well-known that B(-), formed by adding one electron to boron, is isoelectronic to carbon, cluster studies have considerably expanded the possibilities of new structures and new materials using the B(-)/C analogy. It is believed that the electronic transmutation concept will be effective and valuable in aiding the design of new boride materials with predictable properties. The study of boron clusters with intermediate properties between those of individual atoms and bulk solids has given rise to a unique opportunity to broaden the frontier of boron chemistry. Understanding boron clusters has spurred experimentalists and theoreticians to find new boron-based nanomaterials, such as boron fullerenes, nanotubes, two-dimensional boron, and new compounds containing boron clusters as building blocks. Here, a brief and timely overview is presented addressing the recent progress made on boron clusters and the approaches used in the authors' laboratories to determine the structure, stability, and chemical bonding of size-selected boron clusters by joint photoelectron spectroscopy and theoretical studies. Specifically, key findings on all-boron hydrocarbon analogues, metal-centered boron wheels, and electronic transmutation in boron clusters are summarized.

Understanding Boron through Size-Selected Clusters: Structure, Chemical Bonding, and Fluxionality

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sergeeva, Alina P.; Popov, Ivan A.; Piazza, Zachary A.

Conspectus Boron is an interesting element with unusual polymorphism. While three-dimensional (3D) structural motifs are prevalent in bulk boron, atomic boron clusters are found to have planar or quasi-planar structures, stabilized by localized two-center–two-electron (2c–2e) σ bonds on the periphery and delocalized multicenter–two-electron (nc–2e) bonds in both σ and π frameworks. Electron delocalization is a result of boron’s electron deficiency and leads to fluxional behavior, which has been observed in B13+ and B19–. A unique capability of the in-plane rotation of the inner atoms against the periphery of the cluster in a chosen direction by employing circularly polarized infrared radiationmore » has been suggested. Such fluxional behaviors in boron clusters are interesting and have been proposed as molecular Wankel motors. The concepts of aromaticity and antiaromaticity have been extended beyond organic chemistry to planar boron clusters. The validity of these concepts in understanding the electronic structures of boron clusters is evident in the striking similarities of the π-systems of planar boron clusters to those of polycyclic aromatic hydrocarbons, such as benzene, naphthalene, coronene, anthracene, or phenanthrene. Chemical bonding models developed for boron clusters not only allowed the rationalization of the stability of boron clusters but also lead to the design of novel metal-centered boron wheels with a record-setting planar coordination number of 10. The unprecedented highly coordinated borometallic molecular wheels provide insights into the interactions between transition metals and boron and expand the frontier of boron chemistry. Another interesting feature discovered through cluster studies is boron transmutation. Even though it is well-known that B–, formed by adding one electron to boron, is isoelectronic to carbon, cluster studies have considerably expanded the possibilities of new structures and new materials using the B–/C analogy. It is believed that the electronic transmutation concept will be effective and valuable in aiding the design of new boride materials with predictable properties. The study of boron clusters with intermediate properties between those of individual atoms and bulk solids has given rise to a unique opportunity to broaden the frontier of boron chemistry. Understanding boron clusters has spurred experimentalists and theoreticians to find new boron-based nanomaterials, such as boron fullerenes, nanotubes, two-dimensional boron, and new compounds containing boron clusters as building blocks. Here, a brief and timely overview is presented addressing the recent progress made on boron clusters and the approaches used in the authors’ laboratories to determine the structure, stability, and chemical bonding of size-selected boron clusters by joint photoelectron spectroscopy and theoretical studies. Specifically, key findings on all-boron hydrocarbon analogues, metal-centered boron wheels, and electronic transmutation in boron clusters are summarized.« less

Electron capture activation of the disulfide bond. The role of the asymmetry and electronegativity.

PubMed

Gámez, José A; Serrano-Andrés, Luis; Yáñez, Manuel

2010-02-07

The effects of electron capture on the structure of XSSX' disulfide derivatives in which the substituents attached to the sulfur atoms have different electronegativites have been investigated at different levels of theory, namely DFT, MP2, QCISD and CASSCF/CASPT2. Although it has been generally assumed that electron attachment to disulfide derivatives leads to a systematic and significant activation of the S-S bond, our results show that this is the case only when the substituents X or X' have low electronegativity. Otherwise, the S-S bond in the anion remains practically unperturbed and only the S-X bond is largely activated or even broken, because the extra electron occupies the sigma*(S-X) rather than the sigma*(S-S) antibonding orbital. Our results also show that S-S activation yields a system with a unique anion, whereas when the S-X activation is significant, two stable anionic species, stretched and bent, are formed.

The physical chemistry of coordinated aqua-, ammine-, and mixed-ligand Co2+ complexes: DFT studies on the structure, energetics, and topological properties of the electron density.

PubMed

Varadwaj, Pradeep R; Marques, Helder M

2010-03-07

Spin-unrestricted DFT-X3LYP/6-311++G(d,p) calculations have been performed on a series of complexes of the form [Co(H(2)O)(6-n)(NH(3))(n)](2+) (n = 0-6) to examine their equilibrium gas-phase structures, energetics, and electronic properties in their quartet electronic ground states. In all cases Co(2+) in the energy-minimised structures is in a pseudo-octahedral environment. The calculations overestimate the Co-O and Co-N bond lengths by 0.04 and 0.08 A, respectively, compared to the crystallographically observed mean values. There is a very small Jahn-Teller distortion in the structure of [Co(H(2)O)(6)](2+) which is in contrast to the very marked distortions observed in most (but not all) structures of this cation that have been observed experimentally. The successive replacement of ligated H(2)O by NH(3) leads to an increase in complex stability by 6 +/- 1 kcal mol(-1) per additional NH(3) ligand. Calculations using UB3LYP give stabilisation energies of the complexes about 5 kcal mol(-1) smaller and metal-ligand bond lengths about 0.005 A longer than the X3LYP values since the X3LYP level accounts for the London dispersion energy contribution to the overall stabilisation energy whilst it is largely missing at the B3LYP level. From a natural population analysis (NPA) it is shown that the formation of these complexes is accompanied by ligand-to-metal charge transfer the extent of which increases with the number of NH(3) ligands in the coordination sphere of Co(2+). From an examination of the topological properties of the electron charge density using Bader's quantum theory of atoms in molecules it is shown that the electron density rho(c) at the Co-O bond critical points is generally smaller than that at the Co-N bond critical points. Hence Co-O bonds are weaker than Co-N bonds in these complexes and the stability increases as NH(3) replaces H(2)O in the metal's coordination sphere. Several indicators, including the sign and magnitude of the Laplacian of the charge density nabla(2)rho(c), the ratio of the local potential and kinetic energy densities, |V(c)|/G(c), the sign of the total energy density H(c), and the delocalisation index delta(Co,X), X = O, N, are used to show that whilst the metal-ligand bonds are predominantly ionic in nature, they gain covalent character as NH(3) replaces H(2)O, and the Co-N bond is significantly more covalent than the Co-O bond. We have shown that the delocalisation index delta(Co,X), X = O, N, is strongly correlated with the zero-point corrected stabilisation energy E demonstrating that delta can be used as a measure of the bond stability in these complexes.

Structures and bonding of C2X2Y q (X=Si,Ge,Sn,Pb; Y=C,Si,Ge,Sn,Pb; q = +1,0,-1): π-type templates for planar tetracoordinate heavier group 14 atoms

NASA Astrophysics Data System (ADS)

Yu, Shuang; Sui, Jing-jing; Xu, Jing; Ding, Yi-hong

2018-05-01

Contrasting the big family of the planar tetracoordinate carbon (ptC), species featuring the planar tetracoordinate heavier group element M (ptM) have been largely limited. Effective structural frameworks to accommodate such ptM centres are thus highly desired. In the present article, we report an extensive computational study on 60 pentatomic systems C2X2Yq (X=Si,Ge,Sn,Pb; Y=C,Si,Ge,Sn,Pb; q = +1,0,-1) covering both the low and high spin states. Up to 34 systems were shown to have the very low-lying singlet planar tetracoordinate heavier group 14 (ptM with M=Si,Ge,Sn,Pb) structures bearing the 19 (q = +1), 20 (q = 0) and 21 (q = -1) valence electrons (ve). Structural and bonding analysis confirmed the effectiveness of the inherent π-type ligand skeleton XCCX or XCCY that each have several sets of π-bonding orbitals to stabilise the ptM centre. The structural and bonding motifs of these ptMs differ greatly from the classic ptMs, which have the σ-type ligand skeleton, smaller number of valence electrons (≤18ve), and the centre → ligand π-delocalisation.

James Webb Space Telescope (JWST) Integrated Science Instruments Module (ISIM) Electronics Compartment (IEC) Conformal Shields Composite Bond Structure Qualification Test Method

NASA Technical Reports Server (NTRS)

Yew, Calinda; Stephens, Matt

2015-01-01

The JWST IEC conformal shields are mounted onto a composite frame structure that must undergo qualification testing to satisfy mission assurance requirements. The composite frame segments are bonded together at the joints using epoxy, EA 9394. The development of a test method to verify the integrity of the bonded structure at its operating environment introduces challenges in terms of requirements definition and the attainment of success criteria. Even though protoflight thermal requirements were not achieved, the first attempt in exposing the structure to cryogenic operating conditions in a thermal vacuum environment resulted in approximately 1 bonded joints failure during mechanical pull tests performed at 1.25 times the flight loads. Failure analysis concluded that the failure mode was due to adhesive cracks that formed and propagated along stress concentrated fillets as a result of poor bond squeeze-out control during fabrication. Bond repairs were made and the structures successfully re-tested with an improved LN2 immersion test method to achieve protoflight thermal requirements.

Tungsten Hydride Phosphorus- and Arsenic-Bearing Molecules with Double and Triple W-P and W-As Bonds.

PubMed

Andrews, Lester; Cho, Han-Gook; Fang, Zongtang; Vasiliu, Monica; Dixon, David A

2018-05-07

Laser ablation of tungsten metal provides W atoms which react with phosphine and arsine during condensation in excess argon and neon, leading to major new infrared (IR) absorptions. Annealing, UV irradiation, and deuterium substitution experiments coupled with electronic structure calculations at the density functional theory level led to the assignment of the observed IR absorptions to the E≡WH 3 and HE═WH 2 molecules for E = P and As. The potential energy surfaces for hydrogen transfer from PH 3 to the W were calculated at the coupled-cluster CCSD(T)/complete basis set level. Additional weak bands in the phosphide and arsenide W-H stretching region are assigned to the molecules with loss of H from W, E≡WH 2 . The electronic structure calculations show that the E≡WH 3 molecules have a W-E triple bond, the HE═WH 2 molecules have a W-E double bond, and the H 2 E-WH molecules have a W-E single bond. The formation of multiple E-W bonds leads to increasing stability for the isomers.

Enhancing Protein Disulfide Bond Cleavage by UV Excitation and Electron Capture Dissociation for Top-Down Mass Spectrometry.

PubMed

Wongkongkathep, Piriya; Li, Huilin; Zhang, Xing; Loo, Rachel R Ogorzalek; Julian, Ryan R; Loo, Joseph A

2015-11-15

The application of ion pre-activation with 266 nm ultraviolet (UV) laser irradiation combined with electron capture dissociation (ECD) is demonstrated to enhance top-down mass spectrometry sequence coverage of disulfide bond containing proteins. UV-based activation can homolytically cleave a disulfide bond to yield two separated thiol radicals. Activated ECD experiments of insulin and ribonuclease A containing three and four disulfide bonds, respectively, were performed. UV-activation in combination with ECD allowed the three disulfide bonds of insulin to be cleaved and the overall sequence coverage to be increased. For the larger sized ribonuclease A with four disulfide bonds, irradiation from an infrared laser (10.6 µm) to disrupt non-covalent interactions was combined with UV-activation to facilitate the cleavage of up to three disulfide bonds. Preferences for disulfide bond cleavage are dependent on protein structure and sequence. Disulfide bonds can reform if the generated radicals remain in close proximity. By varying the time delay between the UV-activation and the ECD events, it was determined that disulfide bonds reform within 10-100 msec after their UV-homolytic cleavage.

Silicon-carbon bond inversions driven by 60-keV electrons in graphene.

PubMed

Susi, Toma; Kotakoski, Jani; Kepaptsoglou, Demie; Mangler, Clemens; Lovejoy, Tracy C; Krivanek, Ondrej L; Zan, Recep; Bangert, Ursel; Ayala, Paola; Meyer, Jannik C; Ramasse, Quentin

2014-09-12

We demonstrate that 60-keV electron irradiation drives the diffusion of threefold-coordinated Si dopants in graphene by one lattice site at a time. First principles simulations reveal that each step is caused by an electron impact on a C atom next to the dopant. Although the atomic motion happens below our experimental time resolution, stochastic analysis of 38 such lattice jumps reveals a probability for their occurrence in a good agreement with the simulations. Conversions from three- to fourfold coordinated dopant structures and the subsequent reverse process are significantly less likely than the direct bond inversion. Our results thus provide a model of nondestructive and atomically precise structural modification and detection for two-dimensional materials.

Cooperative Metal+Ligand Oxidative Addition and Sigma-Bond Metathesis: A DFT Study

DOE PAGES

Lopez, Kent G.; Cundari, Thomas R.; Gary, J. Brannon

2018-01-17

A computational study of the experimentally proposed mechanism of alkyne diboration by a PDICo complex yielded two fundamental catalytic steps that undergo remarkable electronic changes, PDI = bis(imino)-pyridine. The reactions are envisaged via DFT (density functional theory) and MCSCF (multi-configuration self-consistent field) simulations as (i) a cooperative metal+ligand oxidative addition, and (ii) a sigma-bond metathesis induced ligand-to-metal charge transfer. Analysis of the bonding of pertinent intermediates/TSs also yielded important insight that may be illuminating with regards to the larger field of green catalysis that seeks to ennoble base metals through synergy with potentially redox non-innocent (RNI) ligands. For the presentmore » case, massive changes in electronic structure do not incur massive energetic penalties. Finally, in conjunction with previous research, one may postulate that structural and energetic “fluidity” among several electronic states of RNI-M 3d along the reaction coordinate is an essential signature of redox cooperativity and thus ennoblement.« less

Cooperative Metal+Ligand Oxidative Addition and Sigma-Bond Metathesis: A DFT Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lopez, Kent G.; Cundari, Thomas R.; Gary, J. Brannon

A computational study of the experimentally proposed mechanism of alkyne diboration by a PDICo complex yielded two fundamental catalytic steps that undergo remarkable electronic changes, PDI = bis(imino)-pyridine. The reactions are envisaged via DFT (density functional theory) and MCSCF (multi-configuration self-consistent field) simulations as (i) a cooperative metal+ligand oxidative addition, and (ii) a sigma-bond metathesis induced ligand-to-metal charge transfer. Analysis of the bonding of pertinent intermediates/TSs also yielded important insight that may be illuminating with regards to the larger field of green catalysis that seeks to ennoble base metals through synergy with potentially redox non-innocent (RNI) ligands. For the presentmore » case, massive changes in electronic structure do not incur massive energetic penalties. Finally, in conjunction with previous research, one may postulate that structural and energetic “fluidity” among several electronic states of RNI-M 3d along the reaction coordinate is an essential signature of redox cooperativity and thus ennoblement.« less

Ionic ASi{sub 2}N{sub 3} (A=Li, Na, K and Rb) stabilized by the covalent Si–N bonding: First-principles calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Huijun; Ren, Jiadong, E-mail: jdren@ysu.edu.cn; Wu, Lailei

The structural, elastic and electronic properties of LiSi{sub 2}N{sub 3} and its substitutions by Na, K and Rb were investigated through first-principles computations. The expansion of lattice parameters of ASi{sub 2}N{sub 3} from Li, Na, K to Rb is found to be determined by the bond angle of Si–N1–Si, which suggests a possible way to improve the lithium ionic conductivity by substitutions. ASi{sub 2}N{sub 3} (A=Li, Na, K and Rb) shows the similar elastic behaviors, while the electronic band gap gradually decreases from 5.1 to 3.4 eV from LiSi{sub 2}N{sub 3} to RbSi{sub 2}N{sub 3}. Interestingly, the analysis of electronicmore » structure, crystal orbital Hamiltonian populations and Bader charges shows that the covalence of Si–N bonding is critical for the stability of ASi{sub 2}N{sub 3} phase. Among ASi{sub 2}N{sub 3} phases, there is a relatively high ionicity in NaSi{sub 2}N{sub 3}; the Si–N bond strength in [Si{sub 2}N{sub 3}]{sup −} net for KSi{sub 2}N{sub 3} and RbSi{sub 2}N{sub 3} is comparable to LiSi{sub 2}N{sub 3}, but stronger than NaSi{sub 2}N{sub 3}. - Graphic abstract: Universal trend of structural and electronic properties in alkaline metal silicon nitrides, ASi{sub 2}N{sub 3}, A=Li, Na, K and Rb. - Highlights: • Trend in structure, electronic and mechanical properties of ASi{sub 2}N{sub 3} (A=Li-Rb) were predicted. • Lattice expansion of ASi{sub 2}N{sub 3} induced by the bond angle of Si–N1–Si was found. • Calculated band gap decreases from 5.1 to 3.4 eV from LiSi{sub 2}N{sub 3} to RbSi{sub 2}N{sub 3}. • Covalent Si–N bonding is critical for the stability of ASi{sub 2}N{sub 3}.« less

Single-crystal X-ray diffraction study of SrGeO3 high-pressure perovskite phase at 100 K

NASA Astrophysics Data System (ADS)

Nakatsuka, Akihiko; Arima, Hiroshi; Ohtaka, Osamu; Fujiwara, Keiko; Yoshiasa, Akira

2017-10-01

Single-crystal X-ray diffraction study of SrGeO3 perovskite (cubic; space group Pmɜ¯m) synthesized at 6 GPa and 1223 K was conducted at a low temperature of 100 K. The residual electron density revealed the presence of the bonding electron at the center of the Ge-O bond, in accordance with our previous conclusion that the Ge-O bond is strongly covalent. From comparison with our previous structure-refinement result at 296 K, the mean square displacement (MSD) of the O atom in the direction of the Ge-O bond is suggested to exhibit no significant temperature dependence, in contrast to that in the direction perpendicular to the bond. Thus, the strong covalency of the Ge-O bond can have a large influence on the temperature dependence of thermal vibration of the O atom.

Thinking Like a Chemist: Intuition in Thermoelectric Materials.

PubMed

Zeier, Wolfgang G; Zevalkink, Alex; Gibbs, Zachary M; Hautier, Geoffroy; Kanatzidis, Mercouri G; Snyder, G Jeffrey

2016-06-06

The coupled transport properties required to create an efficient thermoelectric material necessitates a thorough understanding of the relationship between the chemistry and physics in a solid. We approach thermoelectric material design using the chemical intuition provided by molecular orbital diagrams, tight binding theory, and a classic understanding of bond strength. Concepts such as electronegativity, band width, orbital overlap, bond energy, and bond length are used to explain trends in electronic properties such as the magnitude and temperature dependence of band gap, carrier effective mass, and band degeneracy and convergence. The lattice thermal conductivity is discussed in relation to the crystal structure and bond strength, with emphasis on the importance of bond length. We provide an overview of how symmetry and bonding strength affect electron and phonon transport in solids, and how altering these properties may be used in strategies to improve thermoelectric performance. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-Resolution Infrared and Electron-Diffraction Studies of Trimethylenecyclopropane ([3]-Radialene)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wright, Corey; Holmes, Joshua; Nibler, Joseph W.

2013-05-16

Combined high-resolution spectroscopic, electron-diffraction, and quantum theoretical methods are particularly advantageous for small molecules of high symmetry and can yield accurate structures that reveal subtle effects of electron delocalization on molecular bonds. The smallest of the radialene compounds, trimethylenecyclopropane, [3]-radialene, has been synthesized and examined in the gas phase by these methods. The first high-resolution infrared spectra have been obtained for this molecule of D3h symmetry, leading to an accurate B0 rotational constant value of 0.1378629(8) cm-1, within 0.5% of the value obtained from electronic structure calculations (density functional theory (DFT) B3LYP/cc-pVTZ). This result is employed in an analysis ofmore » electron-diffraction data to obtain the rz bond lengths (in Å): C-H = 1.072 (17), C-C = 1.437 (4), and C=C = 1.330 (4). The analysis does not lead to an accurate value of the HCH angle; however, from comparisons of theoretical and experimental angles for similar compounds, the theoretical prediction of 117.5° is believed to be reliable to within 2°. The effect of electron delocalization in radialene is to reduce the single C-C bond length by 0.07 Å compared to that in cyclopropane.« less

Alkali metal mediated C–C bond coupling reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tachikawa, Hiroto, E-mail: hiroto@eng.hokudai.ac.jp

2015-02-14

Metal catalyzed carbon-carbon (C–C) bond formation is one of the important reactions in pharmacy and in organic chemistry. In the present study, the electron and hole capture dynamics of a lithium-benzene sandwich complex, expressed by Li(Bz){sub 2}, have been investigated by means of direct ab-initio molecular dynamics method. Following the electron capture of Li(Bz){sub 2}, the structure of [Li(Bz){sub 2}]{sup −} was drastically changed: Bz–Bz parallel form was rapidly fluctuated as a function of time, and a new C–C single bond was formed in the C{sub 1}–C{sub 1}′ position of Bz–Bz interaction system. In the hole capture, the intermolecular vibrationmore » between Bz–Bz rings was only enhanced. The mechanism of C–C bond formation in the electron capture was discussed on the basis of theoretical results.« less

IR-UV double resonance spectroscopic investigation of phenylacetylene-alcohol complexes. Alkyl group induced hydrogen bond switching.

PubMed

Singh, Prashant Chandra; Patwari, G Naresh

2008-06-12

The electronic transitions of phenylacetylene complexes with water and trifluoroethanol are shifted to the blue, while the corresponding transitions for methanol and ethanol complexes are shifted to the red relative to the phenylacetylene monomer. Fluorescence dip infrared (FDIR) spectra in the O-H stretching region indicate that, in all the cases, phenylacetylene is acting as a hydrogen bond acceptor to the alcohols. The FDIR spectrum in the acetylenic C-H stretching region shows Fermi resonance bands for the bare phenylacetylene, which act as a sensitive tool to probe the intermolecular structures. The FDIR spectra reveal that water and trifluoroethanol interact with the pi electron density of the acetylene C-C triple bond, while methanol and ethanol interact with the pi electron density of the benzene ring. It can be inferred that the hydrogen bonding acceptor site on phenylacetylene switches from the acetylene pi to the benzene pi with lowering in the partial charge on the hydrogen atom of the OH group. The most significant finding is that the intermolecular structures of water and methanol complexes are notably distinct, which, to the best of our knowledge, this is first such observation in the case of complexes of substituted benzenes.

Interplay between theory and experiment: computational organometallic and transition metal chemistry.

PubMed

Lin, Zhenyang

2010-05-18

Computational and theoretical chemistry provide fundamental insights into the structures, properties, and reactivities of molecules. As a result, theoretical calculations have become indispensable in various fields of chemical research and development. In this Account, we present our research in the area of computational transition metal chemistry, using examples to illustrate how theory impacts our understanding of experimental results and how close collaboration between theoreticians and experimental chemists can be mutually beneficial. We begin by examining the use of computational chemistry to elucidate the details of some unusual chemical bonds. We consider the three-center, two-electron bonding in titanocene sigma-borane complexes and the five-center, four-electron bonding in a rhodium-bismuth complex. The bonding in metallabenzene complexes is also examined. In each case, theoretical calculations provide particular insight into the electronic structure of the chemical bonds. We then give an example of how theoretical calculations aided the structural determination of a kappa(2)-N,N chelate ruthenium complex formed upon heating an intermediate benzonitrile-coordinated complex. An initial X-ray diffraction structure proposed on the basis of a reasonable mechanism appeared to fit well, with an apparently acceptable R value of 0.0478. But when DFT calculations were applied, the optimized geometry differed significantly from the experimental data. By combining experimental and theoretical outlooks, we posited a new structure. Remarkably, a re-refining of the X-ray diffraction data based on the new structure resulted in a slightly lower R value of 0.0453. We further examine the use of computational chemistry in providing new insight into C-H bond activation mechanisms and in understanding the reactivity properties of nucleophilic boryl ligands, addressing experimental difficulties with calculations and vice versa. Finally, we consider the impact of theoretical insights in three very specific experimental studies of chemical reactions, illustrating how theoretical results prompt further experimental studies: (i) diboration of aldehydes catalyzed by copper(I) boryl complexes, (ii) ruthenium-catalyzed C-H amination of arylazides, and (iii) zinc reduction of a vinylcarbyne complex. The concepts and examples presented here are intended for nonspecialists, particularly experimentalists. Together, they illustrate some of the achievements that are possible with a fruitful union of experiment and theory.

Activation of CO and CO2 on homonuclear boron bonds of fullerene-like BN cages: first principles study

NASA Astrophysics Data System (ADS)

Sinthika, S.; Kumar, E. Mathan; Surya, V. J.; Kawazoe, Y.; Park, Noejung; Iyakutti, K.; Thapa, Ranjit

2015-12-01

Using density functional theory we investigate the electronic and atomic structure of fullerene-like boron nitride cage structures. The pentagonal ring leads to the formation of homonuclear bonds. The homonuclear bonds are also found in other BN structures having pentagon line defect. The calculated thermodynamics and vibrational spectra indicated that, among various stable configurations of BN-60 cages, the higher number of homonuclear N-N bonds and lower B:N ratio can result in the more stable structure. The homonuclear bonds bestow the system with salient catalytic properties that can be tuned by modifying the B atom bonding environment. We show that homonuclear B-B (B2) bonds can anchor both oxygen and CO molecules making the cage to be potential candidates as catalyst for CO oxidation via Langmuir-Hinshelwood (LH) mechanism. Moreover, the B-B-B (B3) bonds are reactive enough to capture, activate and hydrogenate CO2 molecules to formic acid. The observed trend in reactivity, viz B3 > B2 > B1 is explained in terms of the position of the boron defect state relative to the Fermi level.

Activation of CO and CO2 on homonuclear boron bonds of fullerene-like BN cages: first principles study

PubMed Central

Sinthika, S.; Kumar, E. Mathan; Surya, V. J.; Kawazoe, Y.; Park, Noejung; Iyakutti, K.; Thapa, Ranjit

2015-01-01

Using density functional theory we investigate the electronic and atomic structure of fullerene-like boron nitride cage structures. The pentagonal ring leads to the formation of homonuclear bonds. The homonuclear bonds are also found in other BN structures having pentagon line defect. The calculated thermodynamics and vibrational spectra indicated that, among various stable configurations of BN-60 cages, the higher number of homonuclear N-N bonds and lower B:N ratio can result in the more stable structure. The homonuclear bonds bestow the system with salient catalytic properties that can be tuned by modifying the B atom bonding environment. We show that homonuclear B-B (B2) bonds can anchor both oxygen and CO molecules making the cage to be potential candidates as catalyst for CO oxidation via Langmuir–Hinshelwood (LH) mechanism. Moreover, the B-B-B (B3) bonds are reactive enough to capture, activate and hydrogenate CO2 molecules to formic acid. The observed trend in reactivity, viz B3 > B2 > B1 is explained in terms of the position of the boron defect state relative to the Fermi level. PMID:26626147

Activation of CO and CO2 on homonuclear boron bonds of fullerene-like BN cages: first principles study.

PubMed

Sinthika, S; Kumar, E Mathan; Surya, V J; Kawazoe, Y; Park, Noejung; Iyakutti, K; Thapa, Ranjit

2015-12-02

Using density functional theory we investigate the electronic and atomic structure of fullerene-like boron nitride cage structures. The pentagonal ring leads to the formation of homonuclear bonds. The homonuclear bonds are also found in other BN structures having pentagon line defect. The calculated thermodynamics and vibrational spectra indicated that, among various stable configurations of BN-60 cages, the higher number of homonuclear N-N bonds and lower B:N ratio can result in the more stable structure. The homonuclear bonds bestow the system with salient catalytic properties that can be tuned by modifying the B atom bonding environment. We show that homonuclear B-B (B2) bonds can anchor both oxygen and CO molecules making the cage to be potential candidates as catalyst for CO oxidation via Langmuir-Hinshelwood (LH) mechanism. Moreover, the B-B-B (B3) bonds are reactive enough to capture, activate and hydrogenate CO2 molecules to formic acid. The observed trend in reactivity, viz B3 > B2 > B1 is explained in terms of the position of the boron defect state relative to the Fermi level.

Thermal transfer structures coupling electronics card(s) to coolant-cooled structure(s)

DOEpatents

David, Milnes P; Graybill, David P; Iyengar, Madhusudan K; Kamath, Vinod; Kochuparambil, Bejoy J; Parida, Pritish R; Schmidt, Roger R

2014-12-16

Cooling apparatuses and coolant-cooled electronic systems are provided which include thermal transfer structures configured to engage with a spring force one or more electronics cards with docking of the electronics card(s) within a respective socket(s) of the electronic system. A thermal transfer structure of the cooling apparatus includes a thermal spreader having a first thermal conduction surface, and a thermally conductive spring assembly coupled to the conduction surface of the thermal spreader and positioned and configured to reside between and physically couple a first surface of an electronics card to the first surface of the thermal spreader with docking of the electronics card within a socket of the electronic system. The thermal transfer structure is, in one embodiment, metallurgically bonded to a coolant-cooled structure and facilitates transfer of heat from the electronics card to coolant flowing through the coolant-cooled structure.

Bonding titanium to Rene 41 alloy

NASA Technical Reports Server (NTRS)

Scott, R. W.

1972-01-01

Pair of intermediate materials joined by electron beam welding method welds titanium to Rene 41 alloy. Bond is necessary for combining into one structure high strength-to-density ratio titanium fan blades and temperature resistant nickel-base alloy turbine-buckets in VTOL aircraft lift-fan rotor.

δ-Deuterium Isotope Effects as Probes for Transition-State Structures of Isoprenoid Substrates

PubMed Central

2015-01-01

The biosynthetic pathways to isoprenoid compounds involve transfer of the prenyl moiety in allylic diphosphates to electron-rich (nucleophilic) acceptors. The acceptors can be many types of nucleophiles, while the allylic diphosphates only differ in the number of isoprene units and stereochemistry of the double bonds in the hydrocarbon moieties. Because of the wide range of nucleophilicities of naturally occurring acceptors, the mechanism for prenyltransfer reactions may be dissociative or associative with early to late transition states. We have measured δ-secondary kinetic isotope effects operating through four bonds for substitution reactions with dimethylallyl derivatives bearing deuterated methyl groups at the distal (C3) carbon atom in the double bond under dissociative and associative conditions. Computational studies with density functional theory indicate that the magnitudes of the isotope effects correlate with the extent of bond formation between the allylic moiety and the electron-rich acceptor in the transition state for alkylation and provide insights into the structures of the transition states for associative and dissociative alkylation reactions. PMID:24665882

Laser desorption single-conformation UV and IR spectroscopy of the sulfonamide drug sulfanilamide, the sulfanilamide-water complex, and the sulfanilamide dimer.

PubMed

Uhlemann, Thomas; Seidel, Sebastian; Müller, Christian W

2017-06-07

We have studied the conformational preferences of the sulfonamide drug sulfanilamide, its dimer, and its monohydrated complex through laser desorption single-conformation UV and IR spectroscopy in a molecular beam. Based on potential energy curves for the inversion of the anilinic and the sulfonamide NH 2 groups calculated at DFT level, we suggest that the zero-point level wave function of the sulfanilamide monomer is appreciably delocalized over all four conformer wells. The sulfanilamide dimer, and the monohydrated complex each exhibit a single isomer in the molecular beam. The isomeric structures of the sulfanilamide dimer and the monohydrated sulfanilamide complex were assigned based on their conformer-specific IR spectra in the NH and OH stretch region. Quantum Theory of Atoms in Molecules (QTAIM) analysis of the calculated electron density in the water complex suggests that the water molecule is bound side-on in a hydrogen bonding pocket, donating one O-HO[double bond, length as m-dash]S hydrogen bond and accepting two hydrogen bonds, a NHO and a CHO hydrogen bond. QTAIM analysis of the dimer electron density suggests that the C i symmetry dimer structure exhibits two dominating N-HO[double bond, length as m-dash]S hydrogen bonds, and three weaker types of interactions: two CHO bonds, two CHN bonds, and a chalcogen OO interaction. Most interestingly, the molecular beam dimer structure closely resembles the R dimer unit - the dimer unit with the greatest interaction energy - of the α, γ, and δ crystal polymorphs. Interacting Quantum Atoms analysis provides evidence that the total intermolecular interaction in the dimer is dominated by the short-range exchange-correlation contribution.

A theoretical study on the electronic structures and equilibrium constants evaluation of Deferasirox iron complexes.

PubMed

Salehi, Samie; Saljooghi, Amir Shokooh; Izadyar, Mohammad

2016-10-01

Elemental iron is essential for cellular growth and homeostasis but it is potentially toxic to the cells and tissues. Excess iron can contribute in tumor initiation and tumor growth. Obviously, in iron overload issues using an iron chelator in order to reduce iron concentration seems to be vital. This study presents the density functional theory calculations of the electronic structure and equilibrium constant for iron-deferasirox (Fe-DFX) complexes in the gas phase, water and DMSO. A comprehensive study was performed to investigate the Deferasirox-iron complexes in chelation therapy. Calculation was performed in CAMB3LYP/6-31G(d,p) to get the optimized structures for iron complexes in high and low spin states. Natural bond orbital and quantum theory of atoms in molecules analyses was carried out with B3LYP/6-311G(d,p) to understand the nature of complex bond character and electronic transition in complexes. Electrostatic potential effects on the complexes were evaluated using the CHelpG calculations. The results indicated that higher affinity for Fe(III) is not strictly a function of bond length but also the degree of Fe-X (X=O,N) covalent bonding. Based on the quantum reactivity parameters which have been investigated here, it is possible reasonable design of the new chelators to improve the chelator abilities. Copyright © 2016 Elsevier Ltd. All rights reserved.

Harnessing redox activity for the formation of uranium tris(imido) compounds

NASA Astrophysics Data System (ADS)

Anderson, Nickolas H.; Odoh, Samuel O.; Yao, Yiyi; Williams, Ursula J.; Schaefer, Brian A.; Kiernicki, John J.; Lewis, Andrew J.; Goshert, Mitchell D.; Fanwick, Phillip E.; Schelter, Eric J.; Walensky, Justin R.; Gagliardi, Laura; Bart, Suzanne C.

2014-10-01

Classically, late transition-metal organometallic compounds promote multielectron processes solely through the change in oxidation state of the metal centre. In contrast, uranium typically undergoes single-electron chemistry. However, using redox-active ligands can engage multielectron reactivity at this metal in analogy to transition metals. Here we show that a redox-flexible pyridine(diimine) ligand can stabilize a series of highly reduced uranium coordination complexes by storing one, two or three electrons in the ligand. These species reduce organoazides easily to form uranium-nitrogen multiple bonds with the release of dinitrogen. The extent of ligand reduction dictates the formation of uranium mono-, bis- and tris(imido) products. Spectroscopic and structural characterization of these compounds supports the idea that electrons are stored in the ligand framework and used in subsequent reactivity. Computational analyses of the uranium imido products probed their molecular and electronic structures, which facilitated a comparison between the bonding in the tris(imido) structure and its tris(oxo) analogue.

Ground/bonding for Large Space System Technology (LSST)

NASA Astrophysics Data System (ADS)

Dunbar, W. G.

1980-04-01

The influence of the environment and extravehicular activity remote assembly operations on the grounding and bonding of metallic and nonmetallic structures is discussed. Grounding and bonding philosophy is outlined for the electrical systems and electronic compartments which contain high voltage, high power electrical and electronic equipment. The influence of plasma and particulate on the system was analyzed and the effects of static buildup on the spacecraft electrical system discussed. Conceptual grounding bonding designs are assessed for capability to withstand high current arcs to ground from a high voltage conductor and electromagnetic interference. Also shown were the extravehicular activities required of the space station and or supply spacecraft crew members to join and inspect the ground system using manual on remote assembly construction.

Correlation between valence electronic structure and magnetic properties in RCo5 (R = rare earth) intermetallic compound

NASA Astrophysics Data System (ADS)

Zhi-Qin, Xue; Yong-Quan, Guo

2016-06-01

The magnetisms of RCo5 (R = rare earth) intermetallics are systematically studied with the empirical electron theory of solids and molecules (EET). The theoretical moments and Curie temperatures agree well with experimental ones. The calculated results show strong correlations between the valence electronic structure and the magnetic properties in RCo5 intermetallic compounds. The moments of RCo5 intermetallics originate mainly from the 3d electrons of Co atoms and 4f electrons of rare earth, and the s electrons also affect the magnetic moments by the hybridization of d and s electrons. It is found that moment of Co atom at 2c site is higher than that at 3g site due to the fact that the bonding effect between R and Co is associated with an electron transformation from 3d electrons into covalence electrons. In the heavy rare-earth-based RCo5 intermetallics, the contribution to magnetic moment originates from the 3d and 4f electrons. The covalence electrons and lattice electrons also affect the Curie temperature, which is proportional to the average moment along the various bonds. Project supported by the National Natural Science Foundation of China (Grant No. 11274110).

Communication: Visualization and spectroscopy of defects induced by dehydrogenation in individual silicon nanocrystals

NASA Astrophysics Data System (ADS)

Kislitsyn, Dmitry A.; Mills, Jon M.; Kocevski, Vancho; Chiu, Sheng-Kuei; DeBenedetti, William J. I.; Gervasi, Christian F.; Taber, Benjamen N.; Rosenfield, Ariel E.; Eriksson, Olle; Rusz, Ján; Goforth, Andrea M.; Nazin, George V.

2016-06-01

We present results of a scanning tunneling spectroscopy (STS) study of the impact of dehydrogenation on the electronic structures of hydrogen-passivated silicon nanocrystals (SiNCs) supported on the Au(111) surface. Gradual dehydrogenation is achieved by injecting high-energy electrons into individual SiNCs, which results, initially, in reduction of the electronic bandgap, and eventually produces midgap electronic states. We use theoretical calculations to show that the STS spectra of midgap states are consistent with the presence of silicon dangling bonds, which are found in different charge states. Our calculations also suggest that the observed initial reduction of the electronic bandgap is attributable to the SiNC surface reconstruction induced by conversion of surface dihydrides to monohydrides due to hydrogen desorption. Our results thus provide the first visualization of the SiNC electronic structure evolution induced by dehydrogenation and provide direct evidence for the existence of diverse dangling bond states on the SiNC surfaces.

Ab initio conformational analysis of N-formyl ?-alanine amide including electron correlation

NASA Astrophysics Data System (ADS)

Yu, Ching-Hsing; Norman, Mya A.; Schäfer, Lothar; Ramek, Michael; Peeters, Anik; van Alsenoy, Christian

2001-06-01

The conformational properties of N-formyl L-alanine amide (ALA) were investigated using RMP2/6-311G∗∗ ab initio gradient geometry optimization. One hundred forty four structures of ALA were optimized at 30° grid points in its φ(N-C(α)), ψ(C(α)-C‧) conformational space. Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces, in φ,ψ-space, of bond lengths, bond angles, torsional sensitivity and electrostatic atomic charges. Analyses show that, in agreement with previous studies, the right-handed helical conformation, αR, is not a local energy minimum of the potential energy surface of ALA. Comparisons with protein crystallographic data show that the characteristic differences between geometrical trends in dipeptides and proteins, previously found for ab initio dipeptide structures obtained without electron correlation, are also found in the electron-correlated geometries. In contrast to generally accepted features of force fields used in empirical molecular modeling, partial atomic charges obtained by the CHELPG method are found to be not constant, but to vary significantly throughout the φ,ψ-space. By comparing RHF and MP2 structures, the effects of dispersion forces on ALA were studied, revealing molecular contractions for those conformations, in which small adjustments of torsional angles entail large changes in non-bonded distances.

Identification and Characterization of Molecular Bonding Structures by ab initio Quasi-Atomic Orbital Analyses.

PubMed

West, Aaron C; Duchimaza-Heredia, Juan J; Gordon, Mark S; Ruedenberg, Klaus

2017-11-22

The quasi-atomic analysis of ab initio electronic wave functions in full valence spaces, which was developed in preceding papers, yields oriented quasi-atomic orbitals in terms of which the ab initio molecular wave function and energy can be expressed. These oriented quasi-atomic orbitals are the rigorous ab initio counterparts to the conceptual bond forming atomic hybrid orbitals of qualitative chemical reasoning. In the present work, the quasi-atomic orbitals are identified as bonding orbitals, lone pair orbitals, radical orbitals, vacant orbitals and orbitals with intermediate character. A program determines the bonding characteristics of all quasi-atomic orbitals in a molecule on the basis of their occupations, bond orders, kinetic bond orders, hybridizations and local symmetries. These data are collected in a record and provide the information for a comprehensive understanding of the synergism that generates the bonding structure that holds the molecule together. Applications to a series of molecules exhibit the complete bonding structures that are embedded in their ab initio wave functions. For the strong bonds in a molecule, the quasi-atomic orbitals provide quantitative ab initio amplifications of the Lewis dot symbols. Beyond characterizing strong bonds, the quasi-atomic analysis also yields an understanding of the weak interactions, such as vicinal, hyperconjugative and radical stabilizations, which can make substantial contributions to the molecular bonding structure.

Electronic structure studies of adsorbate-induced surface reconstructions: oxygen on Rh(1 0 0)

NASA Astrophysics Data System (ADS)

Kirsch, Janet E.; Harris, Suzanne

2004-03-01

Solid-state Fenske-Hall band structure calculations have been used to study the electronic structure and bonding that occur on an "asymmetric" clock reconstructed Rh(1 0 0) surface with a half-monolayer of O atom adsorbates. The displacement of the top-layer Rh atoms on reconstructed O/Rh(1 0 0) is similar to that observed when a half-monolayer of C or N atoms adsorb onto clean Ni(1 0 0). Unlike the five-coordinate C or N adsorbates that adsorb into effectively coplanar sites on the Ni(1 0 0) surface, however, O atoms sit well above the Rh surface plane and occupy three-coordinate adsorption sites. The results of these calculations show that the asymmetric clock reconstruction of O/Rh(1 0 0) increases the negative charge localized on the highly electronegative O atoms and strengthens the O-Rh bonding relative to an unreconstructed surface. This suggests that, in contrast to the C(N)/Ni(1 0 0) clock, which appears to be driven primarily by the restoration of metal-metal bonding, the asymmetric O/Rh(1 0 0) clock reconstruction is driven by the optimization of the O atom bonding environment. Comparisons of the O/Rh(1 0 0) and C(N, O)/Ni(1 0 0) surfaces further indicate that the electronegativity and electron count of the adsorbed species, as well as the electron count and physical size of the metal, all play a role in determining the preferred atomic geometries of these adsorbate-covered transition metal surfaces.

The π-Electron Delocalization in 2-Oxazolines Revisited: Quantification and Comparison with Its Analogue in Esters

PubMed Central

Fimberger, Martin; Luef, Klaus P.; Payerl, Claudia; Fischer, Roland C.; Stelzer, Franz; Kállay, Mihály; Wiesbrock, Frank

2015-01-01

The single crystal X-ray analysis of the ester-functionalized 2-oxazoline, methyl 3-(4,5-dihydrooxazol-2-yl)propanoate, revealed π-electron delocalization along the N–C–O segment in the 2-oxazoline pentacycle to significant extent, which is comparable to its counterpart along the O–C–O segment in the ester. Quantum chemical calculations based on the experimental X-ray geometry of the molecule supported the conjecture that the N–C–O segment has a delocalized electronic structure similar to an ester group. The calculated bond orders were 1.97 and 1.10 for the N=C and C–O bonds, and the computed partial charges for the nitrogen and oxygen atoms of −0.43 and −0.44 were almost identical. In the ester group, the bond orders were 1.94 and 1.18 for the C–O bonds, while the partial charges of the oxygen atom are −0.49 and −0.41, which demonstrates the similar electronic structure of the N–C–O and O–C–O segments. In 2-oxazolines, despite the higher electronegativity of the oxygen atom (compared to the nitrogen atom), the charges of the hetero atoms oxygen and nitrogen are equalized due to the delocalization, and it also means that a cationic attack on the nitrogen is possible, enabling regioselectivity during the initiation of the cationic ring-opening polymerization of 2-oxazoline monomers, which is a prerequisite for the synthesis of materials with well-defined structures. PMID:28184258

A distal point mutation in the streptavidin-biotin complex preserves structure but diminishes binding affinity: experimental evidence of electronic polarization effects?

PubMed

Baugh, Loren; Le Trong, Isolde; Cerutti, David S; Gülich, Susanne; Stayton, Patrick S; Stenkamp, Ronald E; Lybrand, Terry P

2010-06-08

We have identified a distal point mutation in streptavidin that causes a 1000-fold reduction in biotin binding affinity without disrupting the equilibrium complex structure. The F130L mutation creates a small cavity occupied by a water molecule; however, all neighboring side chain positions are preserved, and protein-biotin hydrogen bonds are unperturbed. Molecular dynamics simulations reveal a reduced mobility of biotin binding residues but no observable destabilization of protein-ligand interactions. Our combined structural and computational studies suggest that the additional water molecule may affect binding affinity through an electronic polarization effect that impacts the highly cooperative hydrogen bonding network in the biotin binding pocket.

Geometry at the aliphatic tertiary carbon atom: computational and experimental test of the Walsh rule.

PubMed

Böhm, Stanislav; Exner, Otto

2004-02-01

The geometrical parameters of molecules of 2-substituted 2-methylpropanes and 1-substituted bicyclo[2.2.2]octanes were calculated at the B3LYP/6-311+G(d,p) level. They agreed reasonably well with the mean crystallographic values retrieved from the Cambridge Structural Database for a set of diverse non-cyclic structures with a tertiary C atom. The angle deformations at this C atom produced by the immediately bonded substituent are also closely related to those observed previously in benzene mono derivatives (either as calculated or as derived from crystallographic data). The calculated geometrical parameters were used to test the classical Walsh rule: It is evidently true that an electron-attracting substituent increases the proportion of C-atom p-electrons in the bond to the substituent and leaves more s-electrons to the remaining bonds; as a consequence the C-C-C angles at a tertiary carbon are widened and the C-C bonds shortened. However, this rule describes only part of the reality since the bond angles and lengths are controlled by other factors as well, for instance by steric crowding. Another imperfection of the Walsh rule is that the sequence of substituents does not correspond to their electronegativities, as measured by any known scale; more probably it is connected with the inductive effect, but then only very roughly.

Ordered water structure at hydrophobic graphite interfaces observed by 4D, ultrafast electron crystallography

PubMed Central

Yang, Ding-Shyue; Zewail, Ahmed H.

2009-01-01

Interfacial water has unique properties in various functions. Here, using 4-dimensional (4D), ultrafast electron crystallography with atomic-scale spatial and temporal resolution, we report study of structure and dynamics of interfacial water assembly on a hydrophobic surface. Structurally, vertically stacked bilayers on highly oriented pyrolytic graphite surface were determined to be ordered, contrary to the expectation that the strong hydrogen bonding of water on hydrophobic surfaces would dominate with suppressed interfacial order. Because of its terrace morphology, graphite plays the role of a template. The dynamics is also surprising. After the excitation of graphite by an ultrafast infrared pulse, the interfacial ice structure undergoes nonequilibrium “phase transformation” identified in the hydrogen-bond network through the observation of structural isosbestic point. We provide the time scales involved, the nature of ice-graphite structural dynamics, and relevance to properties related to confined water. PMID:19246378

Hydrogen bond strengthening between o-nitroaniline and formaldehyde in electronic excited states: A theoretical study

NASA Astrophysics Data System (ADS)

Yang, Juan; Li, An Yong

2018-06-01

To study the hydrogen bonds upon photoexcited, the time dependent density function method (TD DFT) was performed to investigate the excited state hydrogen bond properties of between o-nitroaniline (ONA) and formaldehyde (CH2O). The optimized structures of the complex and the monomers both in the ground state and the electronically excited states are calculated using DFT and TD DFT method respectively. Quantum chemical calculations of the electronic and vibrational absorption spectra are also carried out by TD DFT method at the different level. The complex ONA⋯CH2O forms the intramolecular hydrogen bond and intermolecular hydrogen bonds. Since the strength of hydrogen bonds can be measured by studying the vibrational absorption spectra of the characteristic groups on the hydrogen bonding acceptor and donor, it evidently confirms that the hydrogen bonds is strengthened in the S1/S2/T1 excited states upon photoexcitation. As a result, the hydrogen bonds cause that the CH stretch frequency of the proton donor CH2O has a blue shift, and the electron excitations leads to a frequency red shift of Ndbnd O and Nsbnd H stretch modes in the o-nitroaniline(ONA) and a small frequency blue shift of CH stretch mode in the formaldehyde(CH2O) in the S1 and S2 excited states. The excited states S1, S2 and T1 are locally excited states where only the ONA moiety is excited, but the CH2O moiety remains in its ground state.

Molecularly Tuning the Radicaloid N-H···O═C Hydrogen Bond.

PubMed

Lu, Norman; Chung, Wei-Cheng; Ley, Rebecca M; Lin, Kwan-Yu; Francisco, Joseph S; Negishi, Ei-Ichi

2016-03-03

Substituent effects on the open shell N-H···O═C hydrogen-bond has never been reported. This study examines how 12 functional groups composed of electron donating groups (EDG), halogen atoms and electron withdrawing groups (EWG) affect the N-H···O═C hydrogen-bond properties in a six-membered cyclic model system of O═C(Y)-CH═C(X)N-H. It is found that group effects on this open shell H-bonding system are significant and have predictive trends when X = H and Y is varied. When Y is an EDG, the N-H···O═C hydrogen-bond is strengthened; and when Y is an EWG, the bond is weakened; whereas the variation in electronic properties of X group do not exhibit a significant impact upon the hydrogen bond strength. The structural impact of the stronger N-H···O═C hydrogen-bond are (1) shorter H and O distance, r(H···O) and (2) a longer N-H bond length, r(NH). The stronger N-H···O═C hydrogen-bond also acts to pull the H and O in toward one another which has an effect on the bond angles. Our findings show that there is a linear relationship between hydrogen-bond angle and N-H···O═C hydrogen-bond energy in this unusual H-bonding system. In addition, there is a linear correlation of the r(H···O) and the hydrogen bond energy. A short r(H···O) distance corresponds to a large hydrogen bond energy when Y is varied. The observed trends and findings have been validated using three different methods (UB3LYP, M06-2X, and UMP2) with two different basis sets.

Raman spectroscopy as a tool to investigate the structure and electronic properties of carbon-atom wires

PubMed Central

Milani, Alberto; Tommasini, Matteo; Russo, Valeria; Li Bassi, Andrea; Lucotti, Andrea; Cataldo, Franco

2015-01-01

Summary Graphene, nanotubes and other carbon nanostructures have shown potential as candidates for advanced technological applications due to the different coordination of carbon atoms and to the possibility of π-conjugation. In this context, atomic-scale wires comprised of sp-hybridized carbon atoms represent ideal 1D systems to potentially downscale devices to the atomic level. Carbon-atom wires (CAWs) can be arranged in two possible structures: a sequence of double bonds (cumulenes), resulting in a 1D metal, or an alternating sequence of single–triple bonds (polyynes), expected to show semiconducting properties. The electronic and optical properties of CAWs can be finely tuned by controlling the wire length (i.e., the number of carbon atoms) and the type of termination (e.g., atom, molecular group or nanostructure). Although linear, sp-hybridized carbon systems are still considered elusive and unstable materials, a number of nanostructures consisting of sp-carbon wires have been produced and characterized to date. In this short review, we present the main CAW synthesis techniques and stabilization strategies and we discuss the current status of the understanding of their structural, electronic and vibrational properties with particular attention to how these properties are related to one another. We focus on the use of vibrational spectroscopy to provide information on the structural and electronic properties of the system (e.g., determination of wire length). Moreover, by employing Raman spectroscopy and surface enhanced Raman scattering in combination with the support of first principles calculations, we show that a detailed understanding of the charge transfer between CAWs and metal nanoparticles may open the possibility to tune the electronic structure from alternating to equalized bonds. PMID:25821689

Role of interatomic bonding in the mechanical anisotropy and interlayer cohesion of CSH crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dharmawardhana, C.C.; Misra, A.; Aryal, S.

2013-10-15

Atomic scale properties of calcium silicate hydrate (CSH), the main binding phase of hardened Portland cement, are not well understood. Over a century of intense research has identified almost 50 different crystalline CSH minerals which are mainly categorized by their Ca/Si ratio. The electronic structure and interatomic bonding in four major CSH crystalline phases with structures close to those found in hardened cement are investigated via ab initio methods. Our result reveals the critical role of hydrogen bonding and importance of specifying precise locations for water molecules. Quantitative analysis of contributions from different bond types to the overall cohesion showsmore » that while the Si-O covalent bonds dominate, the hydrogen bonding and Ca-O bonding are also very significant. Calculated results reveal the correlation between bond topology and interlayer cohesion. The overall bond order density (BOD) is found to be a more critical measure than the Ca/Si ratio in classifying different CSH crystals.« less

A review of defects and disorder in multinary tetrahedrally bonded semiconductors [Defects and disorder in multinary tetrahedrally bonded semiconductors studied by experiment and theory

DOE PAGES

Baranowski, Lauryn L.; Zawadzki, Pawel; Lany, Stephan; ...

2016-11-10

Defects are critical to understanding the electronic properties of semiconducting compounds, for applications such as light-emitting diodes, transistors, photovoltaics, and thermoelectrics. In this review, we describe our work investigating defects in tetrahedrally bonded, multinary semiconductors, and discuss the place of our research within the context of publications by other groups. We applied experimental and theory techniques to understand point defects, structural disorder, and extended antisite defects in one semiconductor of interest for photovoltaic applications, Cu 2SnS 3. We contrast our findings on Cu 2SnS 3 with other chemically related Cu-Sn-S compounds, as well as structurally related compounds such as Cumore » 2ZnSnS 4 and Cu(In,Ga)Se 2. We find that evaluation of point defects alone is not sufficient to understand defect behavior in multinary tetrahedrally bonded semiconductors. In the case of Cu 2SnS 3 and Cu 2ZnSnS 4, structural disorder and entropy-driven cation clustering can result in nanoscale compositional inhomogeneities which detrimentally impact the electronic transport. Therefore, it is not sufficient to assess only the point defect behavior of new multinary tetrahedrally bonded compounds; effects such as structural disorder and extended antisite defects must also be considered. Altogether, this review provides a framework for evaluating tetrahedrally bonded semiconducting compounds with respect to their defect behavior for photovoltaic and other applications, and suggests new materials that may not be as prone to such imperfections.« less

A review of defects and disorder in multinary tetrahedrally bonded semiconductors [Defects and disorder in multinary tetrahedrally bonded semiconductors studied by experiment and theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baranowski, Lauryn L.; Zawadzki, Pawel; Lany, Stephan

Defects are critical to understanding the electronic properties of semiconducting compounds, for applications such as light-emitting diodes, transistors, photovoltaics, and thermoelectrics. In this review, we describe our work investigating defects in tetrahedrally bonded, multinary semiconductors, and discuss the place of our research within the context of publications by other groups. We applied experimental and theory techniques to understand point defects, structural disorder, and extended antisite defects in one semiconductor of interest for photovoltaic applications, Cu 2SnS 3. We contrast our findings on Cu 2SnS 3 with other chemically related Cu-Sn-S compounds, as well as structurally related compounds such as Cumore » 2ZnSnS 4 and Cu(In,Ga)Se 2. We find that evaluation of point defects alone is not sufficient to understand defect behavior in multinary tetrahedrally bonded semiconductors. In the case of Cu 2SnS 3 and Cu 2ZnSnS 4, structural disorder and entropy-driven cation clustering can result in nanoscale compositional inhomogeneities which detrimentally impact the electronic transport. Therefore, it is not sufficient to assess only the point defect behavior of new multinary tetrahedrally bonded compounds; effects such as structural disorder and extended antisite defects must also be considered. Altogether, this review provides a framework for evaluating tetrahedrally bonded semiconducting compounds with respect to their defect behavior for photovoltaic and other applications, and suggests new materials that may not be as prone to such imperfections.« less

Investigation of the gas-phase structure and rotational barrier of trimethylsilyl trifluoromethanesulfonate and comparison with covalent sulfonates

NASA Astrophysics Data System (ADS)

Defonsi Lestard, María E.; Tuttolomondo, María E.; Varetti, Eduardo L.; Wann, Derek A.; Robertson, Heather E.; Rankin, David W. H.; Altabef, Aida Ben

2010-12-01

The molecular structure of trimethylsilyl trifluoromethanesulfonate, CF 3SO 2OSi(CH 3) 3, has been determined in the gas phase from electron-diffraction data supplemented by ab initio (MP2) and DFT calculations using 6-31G(d), 6-311++G(d,p) and 6-311G++(3df,3pd) basis sets. Both experimental and theoretical data indicate that only one gauche conformer is possible by rotating about the O-S bond. The anomeric effect is a fundamental stereoelectronic interaction and presents a profound influence on the electronic geometry. We have investigated the origin of the anomeric effect by means of NBO and AIM analysis. A natural bond orbital analysis showed that the lpπ[O bonded to Si)] → σ *[C-S] hyperconjugative interaction favors the gauche conformation. In addition, comparison of the structural and stereoelectronic properties of the title molecule with those of silyl trifluoromethanesulfonate and methyl trifluoromethanesulfonate has been carried out.

Low-temperature neutron structure determinations of a series of scorpionate complexes of molybdenum containing B sbnd H sbnd Mo agostic bonds

NASA Astrophysics Data System (ADS)

Piccoli, Paula M. B.; Cowan, John A.; Schultz, Arthur J.; Koetzle, Thomas F.; Yap, Glenn P. A.; Trofimenko, Swiatoslaw

2008-11-01

The structures of four dihydrobis(pyrazol-1-yl)borate (Bp) complexes of molybdenum have been determined at low temperature by single crystal neutron diffraction in order to accurately characterize the three-center B sbnd H sbnd Mo agostic bonding. The B sbnd H1A (agostic) distance is found to be elongated by about 0.05-0.08 Å compared to the B sbnd H1B distance (not agostically bound to the metal center). This systematic study of a series of molecules with different substituents on the Bp ligand permits us to examine the effects of electronic and steric factors on the overall structure and bonding, and particularly on the agostic bond. It is observed that a closer approach of H1A to Mo leads to a longer trans-Mo sbnd CO bond distance, analogous to the trans hydride structural effect in hydride complexes. In addition Fenske-Hall calculations were performed on these complexes, and the results are reported herein.

Theoretical investigation of the electronic structure and quantum transport in the graphene-C(111) diamond surface system.

PubMed

Selli, Daniele; Baburin, Igor; Leoni, Stefano; Zhu, Zhen; Tománek, David; Seifert, Gotthard

2013-10-30

We investigate the interaction of a graphene monolayer with the C(111) diamond surface using ab initio density functional theory. To accommodate the lattice mismatch between graphene and diamond, the overlayer deforms into a wavy structure that binds strongly to the diamond substrate. The detached ridges of the wavy graphene overlayer behave electronically as free-standing polyacetylene chains with delocalized π electrons, separated by regions containing only sp(3) carbon atoms covalently bonded to the (111) diamond surface. We performed quantum transport calculations for different geometries of the system to study how the buckling of the graphene layer and the associated bonding to the diamond substrate affect the transport properties. The system displays high carrier mobility along the ridges and a wide transport gap in the direction normal to the ridges. These intriguing, strongly anisotropic transport properties qualify the hybrid graphene-diamond system as a viable candidate for electronic nanodevices.

O2 reduction to H2O by the multicopper oxidases.

PubMed

Solomon, Edward I; Augustine, Anthony J; Yoon, Jungjoo

2008-08-14

In nature the four electron reduction of O2 to H2O is carried out by Cytochrome c oxidase (CcO) and the multicopper oxidases (MCOs). In the former, Cytochrome c provides electrons for pumping protons to produce a gradient for ATP synthesis, while in the MCOs the function is the oxidation of substrates, either organic or metal ions. In the MCOs the reduction of O2 is carried out at a trinuclear Cu cluster (TNC). Oxygen intermediates have been trapped which exhibit unique spectroscopic features that reflect novel geometric and electronic structures. These intermediates have both intact and cleaved O-O bonds, allowing the reductive cleavage of the O-O bond to be studied in detail both experimentally and computationally. These studies show that the topology of the TNC provides a unique geometric and electronic structure particularly suited to carry out this key reaction in nature.

O2 Reduction to H2O by the Multicopper Oxidases

PubMed Central

Solomon, Edward I.; Augustine, Anthony J.; Yoon, Jungjoo

2010-01-01

In nature the four electron reduction of O2 to H2O is carried out by Cytochrome c Oxidase (CcO) and the multicopper oxidases (MCOs). In the former, Cytochrome c provides electrons for pumping protons to produce a gradient for ATP synthesis, while in the MCOs the function is the oxidation of substrates, either organic or metal ions. In the MCOs the reduction of O2 is carried out at a trinuclear Cu cluster (TNC). Oxygen intermediates have been trapped which exhibit unique spectroscopic features that reflect novel geometric and electronic structures. These intermediates have both intact and cleaved O-O bonds, allowing the reductive cleavage of the O-O bond to be studied in detail both experimentally and computationally. These studies show that the topology of the TNC provides a unique geometric and electronic structure particularly suited to carry out this key reaction in Nature. PMID:18648693

The Electronic Structure and Spectra of Triphenylamines Functionalized by Phenylethynyl Groups

NASA Astrophysics Data System (ADS)

Baryshnikov, G. V.; Minaeva, V. A.; Minaev, B. F.; Grigoras, M.

2018-01-01

We study the features of the electronic structure and the IR, UV, and visible spectra of a series of triphenylamines substituted with phenylethynyl groups. The analysis is performed at the level of the density functional theory (DFT) and its nonstationary version in comparison with the experimental data of IR and electron spectroscopy. It is shown that, in the excited state, there is a change in the alternation of single, double, and triple bonds in accordance with the character of bonding and antibonding in the lowest vacant molecular orbital. The gradual introduction of additional phenylethynyl groups does not cause frequency shifts in the IR spectra of the molecules under study, but significantly affects the intensity of the corresponding IR bands. A similar effect is also observed in the electronic-absorption spectra of these compounds. This can be used for optical tuning of triphenylamines as promising materials for organic light-emitting diodes and solar cells.

Visualizing Chemical Bonds in Synthetic Molecules

NASA Astrophysics Data System (ADS)

Collins, Laura C.; Ruth, Anthony; Green, David B.; Janko, Boldizsar; Gomes, Kenjiro K.

The use of synthetic quantum systems makes it possible to study phenomena that cannot be probed by conventional experiments. We created synthetic molecules using atomic manipulation and directly imaged the chemical bonds using tunneling spectroscopy. These synthetic systems allow us to probe the structure and electronic properties of chemical bonds in molecules, including those that would be unstable in nature, with unprecedented detail. The experimental images of electronic states in our synthetic molecules show a remarkable match to the charge distribution predicted by density functional theory calculations. The statistical analysis of the spectroscopy of these molecules can be adapted in the future to quantify aromaticity, which has been difficult to quantify universally thus far due to vague definitions. We can also study anti-aromatic molecules which are unstable naturally, to illuminate the electronic consequences of antiaromaticity.

First-principles study on the structure, elastic properties, hardness and electronic structure of TMB4 (TM=Cr, Re, Ru and Os) compounds

NASA Astrophysics Data System (ADS)

Pan, Y.; Zheng, W. T.; Guan, W. M.; Zhang, K. H.; Fan, X. F.

2013-11-01

The structural formation, elastic properties, hardness and electronic structure of TMB4 (TM=Cr, Re, Ru and Os) compounds are investigated using first-principles approach. The value of C22 for these compounds is almost two times bigger than the C11 and C33. The intrinsic hardness, shear modulus and Young's modulus are calculated to be in a sequence of CrB4>ReB4>RuB4>OsB4, and the Poisson's ratio and B/G ratio of TMB4 follow the order of CrB4

Structures and properties of fluorinated amorphous carbon films

NASA Astrophysics Data System (ADS)

Huang, K. P.; Lin, P.; Shih, H. C.

2004-07-01

Fluorinated amorphous carbon (a-C:F) films were deposited by radio frequency bias assisted microwave plasma electron cyclotron resonance chemical vapor deposition with tetrafluoromethane (CF4) and acetylene (C2H2) as precursors. The deposition process was performed at two flow ratios R=0.90 and R=0.97, where R=CF4/(CF4+C2H2). The samples were annealed at 300 °C for 30 min. in a N2 atmosphere. Both Fourier transform infrared and electron spectroscopy for chemical analyzer were used to characterize the a-C:F film chemical bond and fluorine concentration, respectively. A high resolution electron energy loss spectrometer was applied to detect the electronic structure. The higher CF4 flow ratio (R=0.97) produced more sp3 linear structure, and it made the a-C:F film smoother and softer. A lifetime of around 0.34 μs and an energy gap of ˜2.75 eV were observed in both the as-deposited and after annealing conditions. The short carriers lifetime in the a-C:F film made the photoluminescence peak blueshift. The annealing changed both the structure and composition of the a-C:F film. The type of fluorocarbon bond and electronic structure characterized the mechanical and physical properties of a-C:F film.

First principle study of structural, electronic and fermi surface properties of aluminum praseodymium

NASA Astrophysics Data System (ADS)

Shugani, Mani; Aynyas, Mahendra; Sanyal, S. P.

2018-05-01

We present a structural, Electronic and Fermi surface properties of Aluminum Praseodymium (AlPr) using First-principles density functional calculation by using full potential linearized augmented plane wave (FP-LAPW) method within generalized gradient approximation (GGA). The ground state properties along with electronic and Fermi surface properties are studied. It is found that AlPr is metallic and the bonding between Al and Pr is covalent.

A DFT-D Study on Structural, Electronic, Thermodynamic, and Mechanical Properties of HMX/MPNO Cocrystal under High Pressure

NASA Astrophysics Data System (ADS)

Lin, He; Chen, Jian-Fu; Cui, Yu-Ming; Zhang, Zhen-Jiang; Yang, Dong-Dong; Zhu, Shun-Guan; Li, Hong-Zhen

2017-04-01

An investigation on the structural, electronic, thermodynamic, and mechanical properties of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)/2-methylpyridine-N-oxide (MPNO) cocrystal was carried out from 0 to 100 GPa by using a dispersion-corrected density functional theory (DFT-D) method. Our calculated crystal structure is in excellent agreement with experimental results at ambient pressure. Based on the analysis of lattice parameters, lattice angles, bond lengths, bond angles, and dihedral angles under high pressure, we observe that HMX molecules in the cocrystal bulk are seriously distorted but MPNO molecules remain relatively unchanged. Hydrogen bond lengths are greatly shortened under high pressure. In addition, with the increase in pressure, the bandgap decreases gradually. However, it increases suddenly at 70 GPa. Some important hydrogen bonds between HMX and MPNO are also observed in the density of states spectrum. According to the thermodynamic analysis, this cocrystal is more easily prepared under low pressure. Finally, we characterized its mechanical properties and the results show that this cocrystal is malleable in nature. We expect that this research can provide a fundamental basis for further HMX cocrystal design and preparation.

Correlation of Calculated Halonium Ion Structures with Experimental Product Distributions from Terminal Alkenes: The Effect of Electron-Withdrawing Fluorine Substituents on the Structure and Charge Localization of Halonium Ions (PREPRINT)

DTIC Science & Technology

2006-04-03

2) Substituting a vinyl hydrogen with a fluorine presents an interesting situation for electrophilic reactions. The π-bond is less...reactive toward electrophiles due to the electron-withdrawing effect of the vinyl fluorine . Therefore, carbocations or radical cations are destabilized...NUMBER Distributions from Terminal Alkenes: The Effect of Electron-Withdrawing Fluorine Substituents on the Structure and Charge Localization of

A Structural Model of a P450-Ferredoxin Complex from Orientation-Selective Double Electron-Electron Resonance Spectroscopy.

PubMed

Bowen, Alice M; Johnson, Eachan O D; Mercuri, Francesco; Hoskins, Nicola J; Qiao, Ruihong; McCullagh, James S O; Lovett, Janet E; Bell, Stephen G; Zhou, Weihong; Timmel, Christiane R; Wong, Luet Lok; Harmer, Jeffrey R

2018-02-21

Cytochrome P450 (CYP) monooxygenases catalyze the oxidation of chemically inert carbon-hydrogen bonds in diverse endogenous and exogenous organic compounds by atmospheric oxygen. This C-H bond oxy-functionalization activity has huge potential in biotechnological applications. Class I CYPs receive the two electrons required for oxygen activation from NAD(P)H via a ferredoxin reductase and ferredoxin. The interaction of Class I CYPs with their cognate ferredoxin is specific. In order to reconstitute the activity of diverse CYPs, structural characterization of CYP-ferredoxin complexes is necessary, but little structural information is available. Here we report a structural model of such a complex (CYP199A2-HaPux) in frozen solution derived from distance and orientation restraints gathered by the EPR technique of orientation-selective double electron-electron resonance (os-DEER). The long-lived oscillations in the os-DEER spectra were well modeled by a single orientation of the CYP199A2-HaPux complex. The structure is different from the two known Class I CYP-Fdx structures: CYP11A1-Adx and CYP101A1-Pdx. At the protein interface, HaPux residues in the [Fe 2 S 2 ] cluster-binding loop and the α3 helix and the C-terminus residue interact with CYP199A2 residues in the proximal loop and the C helix. These residue contacts are consistent with biochemical data on CYP199A2-ferredoxin binding and electron transfer. Electron-tunneling calculations indicate an efficient electron-transfer pathway from the [Fe 2 S 2 ] cluster to the heme. This new structural model of a CYP-Fdx complex provides the basis for tailoring CYP enzymes for which the cognate ferredoxin is not known, to accept electrons from HaPux and display monooxygenase activity.

Pressure dependence of electron density distribution and d-p-π hybridization in titanate perovskite ferroelectrics

NASA Astrophysics Data System (ADS)

Yamanaka, Takamitsu; Nakamoto, Yuki; Ahart, Muhtar; Mao, Ho-kwang

2018-04-01

Electron density distributions of PbTi O3 , BaTi O3 , and SrTi O3 were determined by synchrotron x-ray powder diffraction up to 55 GPa at 300 K and ab initio quantum chemical molecular orbital (MO) calculations, together with a combination of maximum entropy method calculations. The intensity profiles of Bragg peaks reveal split atoms in both ferroelectric PbTi O3 and BaTi O3 , reflecting the two possible positions occupied by the Ti atom. The experimentally obtained atomic structure factor was used for the determination of the deformation in electron density and the d-p-π hybridization between dx z (and dy z) of Ti and px (and py) of O in the Ti-O bond. Ab initio MO calculations proved the change of the molecular orbital coupling and of Mulliken charges with a structure transformation. The Mulliken charge of Ti in the Ti O6 octahedron increased in the ionicity with increasing pressure in the cubic phase. The bonding nature is changed with a decrease in the hybridization of the Ti-O bond and the localization of the electron density with increasing pressure. The hybridization decreases with pressure and disappears in the cubic paraelectric phase, which has a much more localized electron density distribution.

Analysis of the electron density features of small boron clusters and the effects of doping with C, P, Al, Si, and Zn: Magic B7P and B8Si clusters

NASA Astrophysics Data System (ADS)

Saha, P.; Rahane, A. B.; Kumar, V.; Sukumar, N.

2016-05-01

Boron atomic clusters show several interesting and unusual size-dependent features due to the small covalent radius, electron deficiency, and higher coordination number of boron as compared to carbon. These include aromaticity and a diverse array of structures such as quasi-planar, ring or tubular shaped, and fullerene-like. In the present work, we have analyzed features of the computed electron density distributions of small boron clusters having up to 11 boron atoms, and investigated the effect of doping with C, P, Al, Si, and Zn atoms on their structural and physical properties, in order to understand the bonding characteristics and discern trends in bonding and stability. We find that in general there are covalent bonds as well as delocalized charge distribution in these clusters. We associate the strong stability of some of these planar/quasiplanar disc-type clusters with the electronic shell closing with effectively twelve delocalized valence electrons using a disc-shaped jellium model. {{{{B}}}9}-, B10, B7P, and B8Si, in particular, are found to be exceptional with very large gaps between the highest occupied molecular orbital and the lowest unoccupied molecular orbital, and these are suggested to be magic clusters.

Cooperative inter- and intra-layer lattice dynamics of photoexcited multi-walled carbon nanotubes studied by ultrafast electron diffraction.

PubMed

Sun, Shuaishuai; Li, Zhongwen; Li, Zi-An; Xiao, Ruijuan; Zhang, Ming; Tian, Huanfang; Yang, Huaixin; Li, Jianqi

2018-04-26

Optical tuning and probing ultrafast structural response of nanomaterials driven by electronic excitation constitute a challenging but promising approach for understanding microscopic mechanisms and applications in microelectromechanical systems and optoelectrical devices. Here we use pulsed electron diffraction in a transmission electron microscope to investigate laser-induced tubular lattice dynamics of multi-walled carbon nanotubes (MWCNTs) with varying laser fluence and initial specimen temperature. Our photoexcitation experiments demonstrate cooperative and inverse collective atomic motions in intralayer and interlayer directions, whose strengths and rates depend on pump fluence. The electron-driven and thermally driven structural responses with opposite amplitudes cause a crossover between intralayer and interlayer directions. Our ab initio calculations support these findings and reveal that electrons excited from π to π* orbitals in a carbon tube weaken the intralayer bonds while strengthening the interlayer bonds along the radial direction. Moreover, by probing the structural dynamics of MWCNTs at initial temperatures of 300 and 100 K, we uncover the concomitance of thermal and nonthermal dynamical processes and their mutual influence in MWCNTs. Our results illustrate the nature of electron-driven nonthermal process and electron-phonon thermalization in the MWCNTs, and bear implications for the intricate energy conversion and transfer in materials at the nanoscale.

Correlation of martensitic transformation temperatures of Ni- Mn-Ga/Al-X alloys to non-bonding electron concentration

NASA Astrophysics Data System (ADS)

Ramudu, M.; Satish Kumar, A.; Seshubai, V.; Rajasekharan, T.

2015-02-01

The martensitic transformation TM of the alloys of Ni-Mn-Ga and Ni-Mn-Al show a general trend of increase with electron per atom ratio (e/a) calculated from the total number of electrons outside the rare gas shell of the atoms. However prediction of TM fails among iron substituted Ni-Mn-Ga alloys and those with In doped for Ga, due to the absence of a useful trend. A scheme of computing modified electron concentration is presented considering only the non-bonding electrons per atom Ne/a of the compounds, based on Pauling's ideas on the electronic structure of metallic elements. Systematic variation of TM with Ne/a is reproduced for a large number of alloys of Ni-Mn-Ga and the anomaly observed for Fe containing alloys with e/a disappears. The non-bonding electron concentration is thus demonstrated to be effective in predicting TM of shape memory alloys of Ni-Mn-Ga-X system including the isoelectronic compounds of Ni-Mn-Ga-In.

Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation

PubMed Central

Serganov, Alexander; Keiper, Sonja; Malinina, Lucy; Tereshko, Valentina; Skripkin, Eugene; Höbartner, Claudia; Polonskaia, Anna; Phan, Anh Tuân; Wombacher, Richard; Micura, Ronald; Dauter, Zbigniew; Jäschke, Andres; Patel, Dinshaw J

2015-01-01

The majority of structural efforts addressing RNA’s catalytic function have focused on natural ribozymes, which catalyze phosphodiester transfer reactions. By contrast, little is known about how RNA catalyzes other types of chemical reactions. We report here the crystal structures of a ribozyme that catalyzes enantioselective carbon-carbon bond formation by the Diels-Alder reaction in the unbound state and in complex with a reaction product. The RNA adopts a λ-shaped nested pseudoknot architecture whose preformed hydrophobic pocket is precisely complementary in shape to the reaction product. RNA folding and product binding are dictated by extensive stacking and hydrogen bonding, whereas stereoselection is governed by the shape of the catalytic pocket. Catalysis is apparently achieved by a combination of proximity, complementarity and electronic effects. We observe structural parallels in the independently evolved catalytic pocket architectures for ribozyme- and antibody-catalyzed Diels-Alder carbon-carbon bond-forming reactions. PMID:15723077

Bond-order potential for magnetic body-centered-cubic iron and its transferability

NASA Astrophysics Data System (ADS)

Lin, Yi-Shen; Mrovec, M.; Vitek, V.

2016-06-01

We derived and thoroughly tested a bond-order potential (BOP) for body-centered-cubic (bcc) magnetic iron that can be employed in atomistic calculations of a broad variety of crystal defects that control structural, mechanical, and thermodynamic properties of this technologically important metal. The constructed BOP reflects correctly the mixed nearly free electron and covalent bonding arising from the partially filled d band as well as the ferromagnetism that is actually responsible for the stability of the bcc structure of iron at low temperatures. The covalent part of the cohesive energy is determined within the tight-binding bond model with the Green's function of the Schrödinger equation determined using the method of continued fractions terminated at a sufficient level of the moments of the density of states. This makes the BOP an O (N ) method usable for very large numbers of particles. Only d d bonds are included explicitly, but the effect of s electrons on the covalent energy is included via their screening of the corresponding d d bonds. The magnetic part of the cohesive energy is included using the Stoner model of itinerant magnetism. The repulsive part of the cohesive energy is represented, as in any tight-binding scheme, by an empirical formula. Its functional form is physically justified by studies of the repulsion in face-centered-cubic (fcc) solid argon under very high pressure where the repulsion originates from overlapping s and p closed-shell electrons just as it does from closed-shell s electrons in transition metals squeezed into the ion core under the influence of the large covalent d bonding. Testing of the transferability of the developed BOP to environments significantly different from those of the ideal bcc lattice was carried out by studying crystal structures and magnetic states alternative to the ferromagnetic bcc lattice, vacancies, divacancies, self-interstitial atoms (SIAs), paths continuously transforming the bcc structure to different less symmetric structures and phonons. The results of these calculations are compared with either experiments or calculations based on the density functional theory (DFT), and they all show very good agreement. Importantly, the lowest energy configuration of SIAs agrees with DFT calculations that show that it is an exception within bcc transition metals controlled by magnetism. Moreover, the migration energy of interstitials is significantly lower than that of vacancies, which is essential for correct analysis of the effects of irradiation. Finally, the core structure and glide of ½ <111 > screw dislocations that control the plastic flow in single crystals of bcc metals was explored. The results fully agree with available DFT based studies and with experimental observations of the slip geometry of bcc iron at low temperatures.

Bond-length distributions for ions bonded to oxygen: results for the non-metals and discussion of lone-pair stereoactivity and the polymerization of PO4

PubMed Central

Gagné, Olivier Charles

2018-01-01

Bond-length distributions are examined for three configurations of the H+ ion, 16 configurations of the group 14–16 non-metal ions and seven configurations of the group 17 ions bonded to oxygen, for 223 coordination polyhedra and 452 bond distances for the H+ ion, 5957 coordination polyhedra and 22 784 bond distances for the group 14–16 non-metal ions, and 248 coordination polyhedra and 1394 bond distances for the group 17 non-metal ions. H⋯O and O—H + H⋯O distances correlate with O⋯O distance (R 2 = 0.94 and 0.96): H⋯O = 1.273 × O⋯O – 1.717 Å; O—H + H⋯O = 1.068 × O⋯O – 0.170 Å. These equations may be used to locate the hydrogen atom more accurately in a structure refined by X-ray diffraction. For non-metal elements that occur with lone-pair electrons, the most observed state between the n versus n+2 oxidation state is that of highest oxidation state for period 3 cations, and lowest oxidation state for period 4 and 5 cations when bonded to O2−. Observed O—X—O bond angles indicate that the period 3 non-metal ions P3+, S4+, Cl3+ and Cl5+ are lone-pair seteroactive when bonded to O2−, even though they do not form secondary bonds. There is no strong correlation between the degree of lone-pair stereoactivity and coordination number when including secondary bonds. There is no correlation between lone-pair stereoactivity and bond-valence sum at the central cation. In synthetic compounds, PO4 polymerizes via one or two bridging oxygen atoms, but not by three. Partitioning our PO4 dataset shows that multi-modality in the distribution of bond lengths is caused by the different bond-valence constraints that arise for Obr = 0, 1 and 2. For strongly bonded cations, i.e. oxyanions, the most probable cause of mean bond length variation is the effect of structure type, i.e. stress induced by the inability of a structure to follow its a priori bond lengths. For ions with stereoactive lone-pair electrons, the most probable cause of variation is bond-length distortion.

How Does Amino Acid Ligand Modulate Au Core Structure and Characteristics in Peptide Coated Au Nanocluster?

PubMed

Li, Nan; Li, Xu; Zhao, Hongkang; Zhao, Lina

2018-03-01

The atomic structures and the corresponding physicochemical properties of peptide coated Au nanoclusters determine their distinctive biological targeting applications. To learn the modulation of amino acid ligand on the atomic structure and electronic characteristics of coated Au core is the fundamental knowledge for peptide coated Au nanocluster design and construction. Based on our recent coated Au nanocluster configuration study (Nanoscale, 2016, 8, 11454), we built the typically simplified Au13(Cys-Au-Cys) system to more clearly learn the basic modulation information of amino acid ligand on Au core by the density functional theory (DFT) calculations. There are two isomers as ligand adjacent bonding (Iso1) and diagonal bonding (Iso2) to Au13 cores. The geometry optimizations indicate the adjacent bonding Iso1 is more stable than Iso2. More important, the Au13 core of Iso1 distorts much more significantly than that of Iso2 by Cys-Au-Cys bonding through the root-mean-square deviation (RMSD) analysis, which modulate their electronic characteristics in different ways. In addition, the frontier molecular orbital results of Au13(Cys-Au-Cys) isomers confirm that the Au cores mainly determine the blue shifts of Au13(Cys-Au-Cys) systems versus the original Au13 core in their UV-visible absorption spectrum studies. The configuration of Au13 core performs deformation under Cys-Au-Cys ligand modulation to reach new stability with distinct atomic structure and electronic properties, which could be the theory basis for peptide coated AuNCs design and construction.

Theoretical studies of structure-property relations in graphene-based carbon nanostructures

NASA Astrophysics Data System (ADS)

Maroudas, Dimitrios

2014-03-01

This presentation focuses on establishing relations between atomic structure, electronic structure, and properties in graphene-based carbon nanostructures through first-principles density functional theory calculations and molecular-dynamics simulations. We have analyzed carbon nanostructure formation from twisted bilayer graphene, upon creation of interlayer covalent C-C bonds due to patterned hydrogenation or fluorination. For small twist angles and twist angles near 30 degrees, interlayer covalent bonding generates superlattices of diamond-like nanocrystals and of fullerene-like configurations, respectively, embedded within the graphene layers. The electronic band gaps of these superlattices can be tuned through selective chemical functionalization and creation of interlayer bonds, and range from a few meV to over 1.2 eV. The mechanical properties of these superstructures also can be precisely tuned by controlling the extent of chemical functionalization. Importantly, the shear modulus is shown to increase monotonically with the fraction of sp3-hybridized C-C bonds. We have also studied collective interactions of multiple defects such as random distributions of vacancies in single-layer graphene (SLG). We find that a crystalline-to-amorphous structural transition occurs at vacancy concentrations of 5-10% over a broad temperature range. The structure of our defect-induced amorphized graphene is in excellent agreement with experimental observations of SLG exposed to a high electron irradiation dose. Simulations of tensile tests on these irradiated graphene sheets identify trends for the ultimate tensile strength, failure strain, and toughness as a function of vacancy concentration. The vacancy-induced amorphization transition is accompanied by a brittle-to-ductile transition in the failure response of irradiated graphene sheets and even heavily damaged samples exhibit tensile strengths near 30 GPa, in significant excess of those typical of engineering materials.

Probing Fe-V Bonding in a C3-Symmetric Heterobimetallic Complex.

PubMed

Greer, Samuel M; McKay, Johannes; Gramigna, Kathryn M; Thomas, Christine M; Stoian, Sebastian A; Hill, Stephen

2018-04-30

Direct metal-metal bonding of two distinct first-row transition metals remains relatively unexplored compared to their second- and third-row heterobimetallic counterparts. Herein, a recently reported Fe-V triply bonded species, [V( i PrNPPh 2 ) 3 FeI] (1; Kuppuswamy, S.; Powers, T. M.; Krogman, J. P.; Bezpalko, M. W.; Foxman, B. M.; Thomas, C. M. Vanadium-iron complexes featuring metal-metal multiple bonds. Chem. Sci. 2013, 4, 3557-3565), is investigated using high-frequency electron paramagnetic resonance, field- and temperature-dependent 57 Fe nuclear gamma resonance (Mössbauer) spectroscopy, and high-field electron-electron double resonance detected nuclear magnetic resonance. From the use of this suite of physical methods, we have assessed the electronic structure of 1. These studies allow us to establish the effective g̃ tensors as well as the Fe/V electro-nuclear hyperfine interaction tensors of the spin S = 1 / 2 ground state. We have rationalized these tensors in the context of ligand field theory supported by quantum chemical calculations. This theoretical analysis suggests that the S = 1 / 2 ground state originates from a single unpaired electron predominately localized on the Fe site.

A theoretical investigation of the structural and electronic properties of 55-atom nanoclusters: The examples of Y-Tc and Pt.

PubMed

Batista, Krys E A; Piotrowski, Maurício J; Chaves, Anderson S; Da Silva, Juarez L F

2016-02-07

Several studies have found that the Pt55 nanocluster adopts a distorted reduced core structure, DRC55, in which there are 8-11 atoms in the core and 47-44 atoms in the surface, instead of the compact and high-symmetry icosahedron structure, ICO55, with 13 and 42 atoms in the core and surface, respectively. The DRC structure has also been obtained as the putative global minimum configuration (GMC) for the Zn55 (3d), Cd55 (4d), and Au55 (5d) systems. Thus, the DRC55 structure has been reported only for systems with a large occupation of the d-states, where the effects of the occupation of the valence anti-bonding d-states might play an important role. Can we observe the DRC structure for 55-atom transition-metal systems with non-occupation of the anti-bonding d-states? To address this question, we performed a theoretical investigation of the Y 55, Zr55, Nb55, Mo55, Tc55, and Pt55 nanoclusters, employing density functional theory calculations. For the putative GMCs, we found that the Y 55 adopts the ICO55 structure, while Nb55 and Mo55 adopt a bulk-like fragment based on the hexagonal close-packed structure and Tc55 adopts a face-centered cubic fragment; however, Zr55 adopts a DRC55 structure, like Zn55, Cd55, Pt55, and Au55. Thus we can conclude that the preference for DRC55 structure is not related to the occupation of the anti-bonding d-states, but to a different effect, in fact, a combination of structural and electronic effects. Furthermore, we obtained that the binding energy per atom follows the occupation of the bonding and anti-bonding model, i.e., the stability of the studied systems increases from Y to Tc with a small oscillation for Mo, which also explains the equilibrium bond lengths. We obtained a larger magnetic moment for Y 55 (31 μB) which can be explained by the localization of the d-states in Y at nanoscale, which is not observed for the remaining systems (0-1 μB).

Chemical lift-off and direct wafer bonding of GaN/InGaN P-I-N structures grown on ZnO

NASA Astrophysics Data System (ADS)

Pantzas, K.; Rogers, D. J.; Bove, P.; Sandana, V. E.; Teherani, F. H.; El Gmili, Y.; Molinari, M.; Patriarche, G.; Largeau, L.; Mauguin, O.; Suresh, S.; Voss, P. L.; Razeghi, M.; Ougazzaden, A.

2016-02-01

p-GaN/i-InGaN/n-GaN (PIN) structures were grown epitaxially on ZnO-buffered c-sapphire substrates by metal organic vapor phase epitaxy using the industry standard ammonia precursor for nitrogen. Scanning electron microscopy revealed continuous layers with a smooth interface between GaN and ZnO and no evidence of ZnO back-etching. Energy Dispersive X-ray Spectroscopy revealed a peak indium content of just under 5 at% in the active layers. The PIN structure was lifted off the sapphire by selectively etching away the ZnO buffer in an acid and then direct bonded onto a glass substrate. Detailed high resolution transmission electron microscoy and grazing incidence X-ray diffraction studies revealed that the structural quality of the PIN structures was preserved during the transfer process.

Resonance bonding in XNgY (X = F, Cl, Br, I; Ng = Kr or Xe; Y = CN or NC) molecules: an NBO/NRT investigation.

PubMed

Song, Junjie; Su, Yue; Jia, Yanping; Chen, Lusheng; Zhang, Guiqiu

2018-05-07

Several noble-gas-containing molecules XNgY were observed experimentally. However, the bonding in such systems is still not understood. Using natural bond orbital and natural resonance theory (NBO/NRT) methods, the present work investigated bonding of the title molecules. The results show that each of the studied XNgY molecules should be better described as a resonance hybrid of ω-bonding and [Formula: see text]-type long-bonding structures: X: - Ng +  - Y, X - Ng + : Y - , and X ^ Y. The ω-bonding and long-bonding make competing contributions to the composite resonance hybrid due to the accurately preserved bond order conservation principle. We find that the resonance bonding is highly tunable for these noble-gas-containing molecules due to its dependence on the nature of the halogen X or the central noble-gas atoms Ng. When the molecule XNgY consists of a relatively lighter Ng atom, a relatively low-electronegative X atom, and the CN fragment rather than NC, the long-bonding structure X ^ Y tends to be highlighted. In contrast, the heavy Ng atom and high-electronegative X atom will enhance the ω-bonding structure. Overall, the present work provides electronic principles and chemical insights that help understand the bonding in these XNgY species.

Bonding in tris(. eta. sup 5 -cyclopentadienyl) actinide complexes. 3. Interaction of. pi. -neutral,. pi. -acidic, and. pi. -basic ligands with (. eta. sup 5 -C sub 5 H sub 5 ) sub 3 U sup 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bursten, B.E.; Rhodes, L.F.; Strittmater

1989-04-12

A qualitative treatment of the bonding in Cp{sub 3}M (Cp = {eta}{sup 5}-C{sub 5}H{sub 5}) compounds under C{sub 3{upsilon}} symmetry reveals that the Cp{sub 3}{sup 3{minus}} ligand field contains a high-lying a{sub 2} orbital which is restricted by symmetry to interact only with metals that contain f orbitals. Quantitative investigation of the electronic structure of 5f{sup 3} Cp{sub 3}U via X{alpha}-SW molecular orbital calculations with quasi-relativistic corrections reveals that the Cp ligands donate electron density primarily into the U 6d orbitals while the three principally metal-based valence electrons are housed in the 5f orbitals. Electronic structure calculations of Cl{sub 3}Umore » show that although Cl can be considered isolobal with Cp, it is a poorer donor ligand. Calculations of Cp{sub 3}U bonded to a fourth ligand L (L = H, CO, NO, OH) indicate that the {sigma}-bonding framework is essentially the same for {pi}-neutral (H), {pi}-acidic (CO, NO), or {pi}-basic (OH) ligands: Electron density is donated from the {sigma} orbital of the fourth ligand into a uranium orbital that is primarily 6d{sub z{sup 2}} in character with minor contributions from the 5f{sub z{sup 3}} orbital, the 7p{sub z} orbital, and the 7s orbital. In the {pi}-bonding framework, the U 5f orbitals are responsible for back-donation into the {pi}* orbitals of CO an NO, while acceptance of electron density from the {pi} orbitals of OH involves the U 6d orbitals and, to a lesser extent, the U 5f orbitals. The bonding scheme of Cp{sub 3}UNO suggests that this molecule may prove to be a rather unusual example of a linear NO{sup {minus}} ligand.« less

The structural, electronic and optical properties of Au-ZnO interface structure from the first-principles calculation

NASA Astrophysics Data System (ADS)

Huo, Jin-Rong; Li, Lu; Cheng, Hai-Xia; Wang, Xiao-Xu; Zhang, Guo-Hua; Qian, Ping

2018-03-01

The interface structure, electronic and optical properties of Au-ZnO are studied using the first-principles calculation based on density functional theory (DFT). Given the interfacial distance, bonding configurations and terminated surface, we built the optimal interface structure and calculated the electronic and optical properties of the interface. The total density of states, partial electronic density of states, electric charge density and atomic populations (Mulliken) are also displayed. The results show that the electrons converge at O atoms at the interface, leading to a stronger binding of interfaces and thereby affecting the optical properties of interface structures. In addition, we present the binding energies of different interface structures. When the interface structure of Au-ZnO gets changed, furthermore, varying optical properties are exhibited.

L-Edge X-ray Absorption Spectroscopic Investigation of {FeNO} 6: Delocalization vs Antiferromagnetic Coupling

DOE PAGES

Yan, James J.; Gonzales, Margarita A.; Mascharak, Pradip K.; ...

2016-12-22

NO is a classic non-innocent ligand, and iron nitrosyls can have different electronic structure descriptions depending on their spin state and coordination environment. These highly covalent ligands are found in metalloproteins and are also used as models for Fe–O 2 systems. Here, this study utilizes iron L-edge X-ray absorption spectroscopy (XAS), interpreted using a valence bond configuration interaction multiplet model, to directly experimentally probe the electronic structure of the S = 0 {FeNO} 6 compound [Fe(PaPy 3)NO] 2+ (PaPy 3 = N,N-bis(2-pyridylmethyl)amine-N-ethyl-2-pyridine-2-carboxamide) and the S = 0 [Fe(PaPy 3)CO] + reference compound. This method allows separation of the σ-donation andmore » π-acceptor interactions of the ligand through ligand-to-metal and metal-to-ligand charge-transfer mixing pathways. The analysis shows that the {FeNO} 6 electronic structure is best described as Fe III–NO(neutral), with no localized electron in an NO π* orbital or electron hole in an Fe dπ orbital. This delocalization comes from the large energy gap between the Fe–NO π-bonding and antibonding molecular orbitals relative to the exchange interactions between electrons in these orbitals. This study demonstrates the utility of L-edge XAS in experimentally defining highly delocalized electronic structures.« less

Atomic structures and electronic properties of 2H-NbSe2: The impact of Ti doping

NASA Astrophysics Data System (ADS)

Li, Hongping; Chen, Lin; Zhang, Kun; Liang, Jiaqing; Tang, Hua; Li, Changsheng; Liu, Xiaojuan; Meng, Jian; Wang, Zhongchang

2014-09-01

Layered transition metal dichalcogenides have aroused renewed interest as electronic materials, yet their electronic performances could be modified by chemical doping. Here, we perform a systematic first-principles calculation to investigate the effect of Ti doping on atomic structure and electronic properties of the 2H-NbSe2. We consider a total of three possible Ti-doping models and find that both the substitution and intercalated models are chemically preferred with the intercalation model being more favorable than the substitution one. Structural analyses reveal a slight lattice distortion triggered by Ti doping, but the original structure of 2H-NbSe2 is maintained. We also observe an expansion of c axis in the substituted model, which is attributed to the reduced van der Waals interaction arising from the increased Se-Se bond length. Our calculations also predict that the electron transport properties can be enhanced by the Ti doping, especially for the Ti-intercalated 2H-NbSe2, which should be beneficial for the realization of superconductivity. Furthermore, the covalence element is found in the Ti-Se bonds, which is ascribed to the hybridization of Ti 3d and Se 4p orbitals. The findings indicate that doping of transition metals can be regarded as a useful way to tailor electronic states so as to improve electron transport properties of 2H-NbSe2.

Origin of structural analogies and differences between the atomic structures of GeSe4 and GeS4 glasses: A first principles study.

PubMed

Bouzid, Assil; Le Roux, Sébastien; Ori, Guido; Boero, Mauro; Massobrio, Carlo

2015-07-21

First-principles molecular dynamics simulations based on density functional theory are employed for a comparative study of structural and bonding properties of two stoichiometrically identical chalcogenide glasses, GeSe4 and GeS4. Two periodic cells of 120 and 480 atoms are adopted. Both glasses feature a coexistence of Ge-centered tetrahedra and Se(S) homopolar connections. Results obtained for N = 480 indicate substantial differences at the level of the Se(S) environment, since Ge-Se-Se connections are more frequent than the corresponding Ge-S-S ones. The presence of a more prominent first sharp diffraction peak in the total neutron structure factor of glassy GeS4 is rationalized in terms of a higher number of large size rings, accounting for extended Ge-Se correlations. Both the electronic density of states and appropriate electronic localization tools provide evidence of a higher ionic character of Ge-S bonds when compared to Ge-Se bonds. An interesting byproduct of these investigations is the occurrence of discernible size effects that affect structural motifs involving next nearest neighbor distances, when 120 or 480 atoms are used.

Structures and chemical bonding of B{sub 3}O{sub 3}{sup −/0} and B{sub 3}O{sub 3}H{sup −/0}: A combined photoelectron spectroscopy and first-principles theory study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Li-Juan; Xu, Hong-Guang; Feng, Gang

We present a combined photoelectron spectroscopy and first-principles theory study on the structural and electronic properties and chemical bonding of B{sub 3}O{sub 3}{sup −/0} and B{sub 3}O{sub 3}H{sup −/0} clusters. The concerted experimental and theoretical data show that the global-minimum structures of B{sub 3}O{sub 3} and B{sub 3}O{sub 3}H neutrals are very different from those of their anionic counterparts. The B{sub 3}O{sub 3}{sup −} anion is characterized to possess a V-shaped OB–B–BO chain with overall C{sub 2v} symmetry (1A), in which the central B atom interacts with two equivalent boronyl (B≡O) terminals via B–B single bonds as well as withmore » one O atom via a B=O double bond. The B{sub 3}O{sub 3}H{sup −} anion has a C{sub s} (2A) structure, containing an asymmetric OB–B–OBO zig-zag chain and a terminal H atom interacting with the central B atom. In contrast, the C{sub 2v} (1a) global minimum of B{sub 3}O{sub 3} neutral contains a rhombic B{sub 2}O{sub 2} ring with one B atom bonded to a BO terminal and that of neutral B{sub 3}O{sub 3}H (2a) is also of C{sub 2v} symmetry, which is readily constructed from C{sub 2v} (1a) by attaching a H atom to the opposite side of the BO group. The H atom in B{sub 3}O{sub 3}H{sup −/0} (2A and 2a) prefers to interact terminally with a B atom, rather than with O. Chemical bonding analyses reveal a three-center four-electron (3c-4e) π hyperbond in the B{sub 3}O{sub 3}H{sup −} (2A) cluster and a four-center four-electron (4c-4e) π bond (that is, the so-called o-bond) in B{sub 3}O{sub 3} (1a) and B{sub 3}O{sub 3}H (2a) neutral clusters.« less

Electronic Structure Studies on the Whole Keplerate Family: Predicting New Members.

PubMed

Melgar, Dolores; Bandeira, Nuno A G; Bo, Carles

2017-04-19

A comprehensive study of the electronic structure of nanoscale molecular oxide capsules of the type [{M VI (M VI ) 5 O 21 } 12 {M' V 2 O 2 (μ-X)(μ-Y)(L n- )} 30 ] (12+n)- is presented, where M,M'=Mo,W, and the bridging ligands X,Y=O,S, carried out by means of density functional theory. Discussion of the electronic structure of these derivatives is focused on the thermodynamic stability of each of the structures, the one having the highest HOMO-LUMO gap being M=W, M'=Mo, X=Y=S. For the most well-known structure M=M'=Mo, X=Y=O, [Mo 132 O 372 ] 12- , the chemical bonding of several ligands to the {Mo V 2 O 2 (μ-O) 2 } linker moiety produces negligible effects on its stability, which is evidence of a strong ionic component in these bonds. The existence of a hitherto unknown species, namely W 132 with both bridging alternatives, is discussed and put into context. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ab initio study on the structural and electronic properties of water surrounding a multifunctional nanoprobe

NASA Astrophysics Data System (ADS)

Xia, Xiuli; Shao, Yuanzhi

2018-02-01

We report the magneto-electric behavior of a dual-modality biomedical nanoprobe, a ternary nanosystem consisting of gold and gadolinia clusters and water molecules, with the effect of both nanoclusters on the structural and electronic properties of water. The hydrogen-oxygen bond lengths and angles as well as electronic charges of water molecules surrounding both nanoclusters were calculated using Hubbard U corrected density functional theory aided by molecular dynamics approach. The calculations reveal existence of a magneto-electric interaction between gold and gadolinium oxide nanoclusters, which influences the physical properties of surrounding water remarkably. A broader (narrower) distribution of Hsbnd O bond lengths (Hsbnd Osbnd H bond angles) was observed at the presence of either gold or gadolinia nanoclusters. The presence of Gd6O9 cluster leads to the larger charges of neighbour oxygen atoms. The distribution of oxygen atom charges becomes border when both Gd6O9 and Au13 clusters coexist. Ab initio calculation provides a feasible approach to explore the most essential interactions among functional components of a multimodal nanoprobe applied in aqueous environment.

Cryosolution infrared study of hydrogen bonded halothane acetylene complex

NASA Astrophysics Data System (ADS)

Melikova, S. M.; Rutkowski, K. S.; Rospenk, M.

2018-05-01

The interactions between halothane (2-bromo-2-chloro-1,1,1-trifluoroethane) and acetylene (C2H2) are studied by FTIR spectroscopy. Results obtained in liquid cryosolutions in Kr suggest weak complex formation stabilized by H - bond. The complexation enthalpy (∼11 kJ/mol) is evaluated in a series of temperature measurements (T ∼ 120-160 K) of integrated intensity of selected bands performed in liquefied Kr. The quantum chemical MP2/6-311++G(2d,2p) calculations predict four different structures of the complex. The most stable and populated (94% at T∼120 K) structure corresponds to the H - bond between H atom of halothane and pi-electron of triple bond between C atoms of acetylene. Wave numbers of vibrational bands of the most stable structure are calculated in anharmonic approximation implemented in Gaussian program.

STRUCTURAL DIVERSITY IN SOLID STATE CHEMISTRY:A Story of Squares and Triangles

NASA Astrophysics Data System (ADS)

Lee, Stephen

1996-10-01

A simple method for calculating the electronic energy of extended solids is discussed in this review. This method is based on the Huckel or tight-binding theory in which an explicit pairwise repulsion is added to the generally attractive forces of the partially filled valence electron bands. An expansion based on the power moments of the electronic density of states is discussed, and the structural energy difference theorem is reviewed. The repulsive energy is found to vary linearly with the second power moment of the electronic density of states. These results are then used to show why there is such a diversity of structure in the solid state. The elemental structures of the main group are rationalized by the above methods. It is the third and fourth power moments (which correspond in part to triangles and squares of bonded atoms) that account for much of the elemental structures of the main group elements of the periodic table. This serves as an introduction to further rationalizations of transition for noble metal alloy, binary and ternary telluride and selenide, and other intermetallic structures.Thus a cohesive picture of both covalent and metallic bonding is presented in this review, illustrating the importance of atomic orbitals and their overlap integrals.

Structural, electronic and magnetic properties of chevron-type graphene, BN and BC{sub 2}N nanoribbons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guerra, T.; Azevedo, S.; Kaschny, J.R.

2017-04-15

Graphene nanoribbons are predicted to be essential components in future nanoelectronics. The size, edge type, arrangement of atoms and width of nanoribbons drastically change their properties. Boronnitrogencarbon nanoribbons properties are not fully understood so far. In the present contribution it was investigated the structural, electronic and magnetic properties of chevron-type carbon, boron nitride and BC{sub 2}N nanoribbons, using first-principles calculations. The results indicate that the structural stability is closely related to the discrepancies in the bond lengths, which can induce structural deformations and stress. Such nanoribbons present a wide range of electronic behaviors, depending on their composition and particularities ofmore » the atomic arrangement. A net magnetic moment is found for structures that present carbon atoms at the nanoribbon borders. Nevertheless, the calculated magnetic moment depends on the peculiarities of the symmetric arrangement of atoms and imbalance of carbon atoms between different sublattices. It was found that all structures which have a significant energy gap do not present magnetic moment, and vice-versa. Such result indicates the strong correlation between the electronic and magnetic properties of the chevron-type nanoribbons. - Highlights: • Small discrepancies between distinct bond lengths can influence the formation energy of the BC{sub 2}N nanoribbons. • The electronic behavior of the BC{sub 2}N chevron-type nanoribbons depends on the atomic arrangement and structural symmetries. • There is a strong correlation between the electronic and magnetic properties for the BC{sub 2}N structures.« less

Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gasparotto, Piero; Ceriotti, Michele, E-mail: michele.ceriotti@epfl.ch

The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding – a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogenmore » bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.« less

Recognizing molecular patterns by machine learning: an agnostic structural definition of the hydrogen bond.

PubMed

Gasparotto, Piero; Ceriotti, Michele

2014-11-07

The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding--a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.

First principles study of the electronic properties and band gap modulation of two-dimensional phosphorene monolayer: Effect of strain engineering

NASA Astrophysics Data System (ADS)

Phuc, Huynh V.; Hieu, Nguyen N.; Ilyasov, Victor V.; Phuong, Le T. T.; Nguyen, Chuong V.

2018-06-01

The effect of strain on the structural and electronic properties of monolayer phosphorene is studied by using first-principle calculations based on the density functional theory. The intra- and inter-bond length and bond angle for monolayer phosphorene is also evaluated. The intra- and inter-bond length and the bond angle for phosphorene show an opposite tendency under different directions of the applied strain. At the equilibrium state, monolayer phosphorene is a semiconductor with a direct band gap at the Γ-point of 0.91 eV. A direct-indirect band gap transition is found in monolayer phosphorene when both the compression and tensile strain are simultaneously applied along both zigzag and armchair directions. Under the applied compression strain, a semiconductor-metal transition for monolayer phosphorene is observed at -13% and -10% along armchair and zigzag direction, respectively. The direct-indirect and phase transition will largely constrain application of monolayer phosphorene to electronic and optical devices.

Phonon Dispersion Measurements of YBa 2Cu 3O 6.15 and YBa 2Cu 3O 6.95 by Time-of-Flight Neutron Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chung, J.-H.; Egami, T.; McQueeny, R. J.

We measured the phonon dispersions of YBa{sub 2}Cu{sub 3}O{sub 6.15} and YBa{sub 2}Cu{sub 3}O{sub 6.95} by time-of-flight inelastic neutron scattering. The in-plane bond-stretching modes in the metallic phase showed a distinct a-b plane anisotropy beyond what is expected for structural origin. Such anisotropy in the longitudinal optical modes, which is absent in the TO, suggests strong in-plane anisotropy in the underlying electronic structure. Apical oxygen bond-stretching modes showed a large frequency change between the insulating and the metallic phases. This large softening also is beyond structural origin, and suggests the effect of local electronic environment.

Transition joints between Zircaloy-2 and stainless steel by diffusion bonding

NASA Astrophysics Data System (ADS)

Bhanumurthy, K.; Krishnan, J.; Kale, G. B.; Banerjee, S.

1994-11-01

The diffusion bonding between Zircaloy-2 and stainless steel (AISI 304L) using niobium, nickel and copper as intermediate layers has been investigated in the temperature range of 750 to 900°C. Bonding was carried out in a vacuum hot press, under compressive loading. Electron probe microanalysis and metallographic analysis showed a good metallurgical compatibility and also indicated the absence of discontunities, micropores and intermetallic compounds at various interfaces. The bond strength of the diffusion bonded assembly was found to be about 400 MPa for the couples bonded at 870°C for 2 h. The dimple structure on the fractured surface is indicative of the ductile mode of failure of the bonded assembly.

Computational simulation of the effects of oxygen on the electronic states of hydrogenated 3C-porous SiC

PubMed Central

2012-01-01

A computational study of the dependence of the electronic band structure and density of states on the chemical surface passivation of cubic porous silicon carbide (pSiC) was performed using ab initio density functional theory and the supercell method. The effects of the porosity and the surface chemistry composition on the energetic stability of pSiC were also investigated. The porous structures were modeled by removing atoms in the [001] direction to produce two different surface chemistries: one fully composed of silicon atoms and one composed of only carbon atoms. The changes in the electronic states of the porous structures as a function of the oxygen (O) content at the surface were studied. Specifically, the oxygen content was increased by replacing pairs of hydrogen (H) atoms on the pore surface with O atoms attached to the surface via either a double bond (X = O) or a bridge bond (X-O-X, X = Si or C). The calculations show that for the fully H-passivated surfaces, the forbidden energy band is larger for the C-rich phase than for the Si-rich phase. For the partially oxygenated Si-rich surfaces, the band gap behavior depends on the O bond type. The energy gap increases as the number of O atoms increases in the supercell if the O atoms are bridge-bonded, whereas the band gap energy does not exhibit a clear trend if O is double-bonded to the surface. In all cases, the gradual oxygenation decreases the band gap of the C-rich surface due to the presence of trap-like states. PMID:22913486

A Chemical Approach to Understanding Oxide Surface Structure and Reactivity

NASA Astrophysics Data System (ADS)

Enterkin, James Andrew

Transmission electron microscopy and diffraction are powerful tools for solving complex structural problems. They complement other analytical techniques, such as x-ray diffraction, elucidating problems which cannot be solved by other techniques. One area where they are of particularly great value is in the determination of surface structures. The research presented herein uses electron microscopy and diffraction as the primary experimental techniques in the development of a chemistry of surface structures. High-resolution electron microscopy revealed that the La4Cu 3MoO12 structure has turbostratic disorder and a lower symmetry space group (Pm) than was previously found. The refinement of the x-ray data was significantly improved by using a disordered model and the Pm space group. A bond valence analysis confirmed that the disordered structure is the superior model. Strontium titanate, SrTiO3, single crystal surfaces were examined principally via transmission electron diffraction. A homologous series with intergrowths was discovered on the (110) surface of strontium titanate, marking the first time that these important concepts of solid state chemistry have been found at the surface. Atmospheric adsorbates, such as H2O and CO2, were found to help to stabilize undercoordinated surface structures on the (100) surface. It was shown that chemical bonding, bond valence, atomic coordination, and stoichiometry greatly influence the development of surface structures. Additionally, such chemistry based analysis was demonstrated to be able to predict surface structure stability and reactivity. Application of a modified Wulff construction to the observed shape of strontium titanate nanocuboids revealed that the surface structure and particle stoichiometry are interlinked, with control over one allowing equally precise control over the other. Platinum nanoparticles on the strontium titanate nanocuboids were shown via high resolution electron microscopy to have cube-on-cube epitaxy, with the shape of the platinum nanoparticles governed by the Winterbottom construction. Precise modification of the support surface will therefore allow engineering of supported metal particles with precise control over which facets are exposed. These results suggest that control over the support surface chemistry can be used to engineer thermodynamically stable, face selective catalysts.

Probing Chemical Bonding and Electronic Structures in ThO- by Anion Photoelectron Imaging and Theoretical Calculations.

PubMed

Li, Yanli; Zou, Jinghan; Xiong, Xiao-Gen; Su, Jing; Xie, Hua; Fei, Zejie; Tang, Zichao; Liu, Hongtao

2017-03-16

Because of renewed research on thorium-based molten salt reactors, there is growing demand and interest in enhancing the knowledge of thorium chemistry both experimentally and theoretically. Compared with uranium, thorium has few chemical studies reported up to the present. Here we report the vibrationally resolved photoelectron imaging of the thorium monoxide anion. The electron affinity of ThO is first reported to be 0.707 ± 0.020 eV. Vibrational frequencies of the ThO molecule and its anion are determined from Franck-Condon simulation. Spectroscopic evidence is obtained for the two-electron transition in ThO - , indicating the strong electron correlation among the (7s σ ) 2 (6d δ ) 1 electrons in ThO - and the (7s σ ) 2 electrons in ThO. These findings are explained by using quantum-chemical calculations including spin-orbit coupling, and the chemical bonding of gaseous ThO molecules is analyzed. The present work will enrich our understanding of bonding capacities with the 6d valence shell.

Electron paramagnetic resonance study of radiation-induced paramagnetic centers in succinic anhydride single crystal

NASA Astrophysics Data System (ADS)

Caliskan, Betul; Caliskan, Ali Cengiz; Er, Emine

2017-09-01

Succinic anhydride single crystals were exposed to 60Co-gamma irradiation at room temperature. The irradiated single crystals were investigated at 125 K by Electron Paramagnetic Resonance (EPR) Spectroscopy. The investigation of EPR spectra of irradiated single crystals of succinic anhydride showed the presence of two succinic anhydride anion radicals. The anion radicals observed in gamma-irradiated succinic anhydride single crystal were created by the scission of the carbon-oxygen double bond. The structure of EPR spectra demonstrated that the hyperfine splittings arise from the same radical species. The reduction of succinic anhydride was identified which is formed by the addition of an electron to oxygen of the Csbnd O bond. The g values, the hyperfine structure constants and direction cosines of the radiation damage centers observed in succinic anhydride single crystal were obtained.

Diazonium functionalized graphene: microstructure, electric, and magnetic properties.

PubMed

Huang, Ping; Jing, Long; Zhu, Huarui; Gao, Xueyun

2013-01-15

The unique honeycomb lattice structure of graphene gives rise to its outstanding electronic properties such as ultrahigh carrier mobility, ballistic transport, and more. However, a crucial obstacle to its use in the electronics industry is its lack of an energy bandgap. A covalent chemistry strategy could overcome this problem, and would have the benefits of being highly controllable and stable in the ambient environment. One possible approach is aryl diazonium functionalization. In this Account, we investigate the micromolecular/lattice structure, electronic structure, and electron-transport properties of nitrophenyl-diazonium-functionalized graphene. We find that nitrophenyl groups mainly adopt random and inhomogeneous configurations on the graphene basal plane, and that their bonding with graphene carbon atoms leads to slight elongation of the graphene lattice spacing. By contrast, hydrogenated graphene has a compressed lattice. Low levels of functionalization suppressed the electric conductivity of the resulting functionalized graphene, while highly functionalized graphene showed the opposite effect. This difference arises from the competition between the charge transfer effect and the scattering enhancement effect introduced by nitrophenyl groups bonding with graphene carbon atoms. Detailed electron transport measurements revealed that the nitrophenyl diazonium functionalization locally breaks the symmetry of graphene lattice, which leads to an increase in the density of state near the Fermi level, thus increasing the carrier density. On the other hand, the bonded nitrophenyl groups act as scattering centers, lowering the mean free path of the charge carriers and suppressing the carrier mobility. In rare cases, we observed ordered configurations of nitrophenyl groups in local domains on graphene flakes due to fluctuations in the reaction processes. We describe one example of such a superlattice, with a lattice constant nearly twice of that of pristine graphene. We performed comprehensive theoretical calculations to investigate the lattice and the electronic structure of the superlattice structure. Our results reveal that it is a thermodynamically stable, spin-polarized semiconductor with a bandgap of ∼0.5 eV. Our results demonstrate the possibility of controlling graphene's electronic properties using aryl diazonium functionalization. Asymmetric addition of aryl groups to different sublattices of graphene is a promising approach for producing ferromagnetic, semiconductive graphene, which will have broad applications in the electronic industry.

Exploring the Interaction Natures in Plutonyl (VI) Complexes with Topological Analyses of Electron Density

PubMed Central

Du, Jiguang; Sun, Xiyuan; Jiang, Gang

2016-01-01

The interaction natures between Pu and different ligands in several plutonyl (VI) complexes are investigated by performing topological analyses of electron density. The geometrical structures in both gaseous and aqueous phases are obtained with B3LYP functional, and are generally in agreement with available theoretical and experimental results when combined with all-electron segmented all-electron relativistic contracted (SARC) basis set. The Pu–Oyl bond orders show significant linear dependence on bond length and the charge of oxygen atoms in plutonyl moiety. The closed-shell interactions were identified for Pu-Ligand bonds in most complexes with quantum theory of atoms in molecules (QTAIM) analyses. Meanwhile, we found that some Pu–Ligand bonds, like Pu–OH−, show weak covalent. The interactive nature of Pu–ligand bonds were revealed based on the interaction quantum atom (IQA) energy decomposition approach, and our results indicate that all Pu–Ligand interactions is dominated by the electrostatic attraction interaction as expected. Meanwhile it is also important to note that the quantum mechanical exchange-correlation contributions can not be ignored. By means of the non-covalent interaction (NCI) approach it has been found that some weak and repulsion interactions existed in plutonyl(VI) complexes, which can not be distinguished by QTAIM, can be successfully identified. PMID:27077844

Metallic cyanoacetylides of copper, silver and gold: generation and structural characterization.

PubMed

Cabezas, Carlos; Barrientos, Carmen; Largo, Antonio; Guillemin, Jean-Claude; Alonso, J L

2016-10-19

The metallic cyanoacetylides CuCCCN, AgCCCN, and AuCCCN have been synthesized in the throat of a pulsed supersonic expansion by reaction of metal vapors, produced by laser ablation, and BrCCCN. Their pure rotational spectra in the (X 1 Σ + ) electronic ground state were observed by Fourier transform microwave spectroscopy in the 2-10 GHz frequency region. Importantly, the rotational spectroscopy constants determined from the analysis of the rotational spectra clearly established the existence of metal-CCCN arrangements for all the mentioned cyanoacetylides. A study of the chemical bonding by means of a topological analysis of the electron density helps to understand the preference for metal-C bonding over metal-N bonding.

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

PubMed

Finazzo, Cinzia; Calle, Carlos; Stoll, Stefan; Van Doorslaer, Sabine; Schweiger, Arthur

2006-04-28

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.

E-H (E = B, Si, C) Bond Activation by Tuning Structural and Electronic Properties of Phosphenium Cations.

PubMed

Đorđević, Nemanja; Ganguly, Rakesh; Petković, Milena; Vidović, Dragoslav

2017-12-04

In this work, strategic enhancement of electrophilicity of phosphenium cations for the purpose of small-molecule activation was described. Our synthetic methodology for generation of novel two-coordinate phosphorus(III)-based compounds [{C 6 H 4 (MeN) 2 C} 2 C·PR] 2+ ([2a] 2+ , R = N i Pr 2 ; [2b] 2+ , R = Ph) was based on the exceptional electron-donating properties of the carbodicarbene ligand (CDC). The effects of P-centered substituent exchange and increase in the overall positive charge on small substrate activation were comparatively determined by incorporating the bis(amino)phosphenium ion [( i Pr 2 N) 2 P] + ([1] + ) in this study. Implemented structural and electronic modifications of phosphenium salts were computationally verified and subsequently confirmed by isolation and characterization of the corresponding E-H (E = B, Si, C) bond activation products. While both phosphenium mono- and dications oxidatively inserted/cleaved the B-H bond of Lewis base stabilized boranes, the increased electrophilicity of doubly charged species also afforded the activation of significantly less hydridic Si-H and C-H bonds. The preference of [2a] 2+ and [2b] 2+ to abstract the hydride rather than to insert into the corresponding bond of silanes, as well as the formation of the carbodicarbene-stabilized parent phosphenium ion [{C 6 H 4 (MeN) 2 C} 2 C·PH 2 ] + ([2·PH 2 ] + ) were experimentally validated.

79/81Br nuclear quadrupole resonance spectroscopic characterization of halogen bonds in supramolecular assemblies† †Electronic supplementary information (ESI) available: 13C SSNMR spectra, powder X-ray diffractograms. See DOI: 10.1039/c8sc01094c

PubMed Central

Cerreia Vioglio, P.; Szell, P. M. J.; Chierotti, M. R.; Gobetto, R.

2018-01-01

Despite the applicability of solid-state NMR to study the halogen bond, the direct NMR detection of 79/81Br covalently bonded to carbon remains impractical due to extremely large spectral widths, even at ultra-high magnetic fields. In contrast, nuclear quadrupole resonance (NQR) offers comparatively sharp resonances. Here, we demonstrate the abilities of 79/81Br NQR to characterize the electronic changes in the C–Br···N halogen bonding motifs found in supramolecular assemblies constructed from 1,4-dibromotetrafluorobenzene and nitrogen-containing heterocycles. An increase in the bromine quadrupolar coupling constant is observed, which correlates linearly with the halogen bond distance (dBr···N). Notably, 79/81Br NQR is able to distinguish between two symmetry-independent halogen bonds in the same crystal structure. This approach offers a rapid and reliable indication for the occurrence of a halogen bond, with experimental times limited only by the observation of 79/81Br NQR resonances. PMID:29899948

Correlation between oxygen adsorption energy and electronic structure of transition metal macrocyclic complexes.

PubMed

Liu, Kexi; Lei, Yinkai; Wang, Guofeng

2013-11-28

Oxygen adsorption energy is directly relevant to the catalytic activity of electrocatalysts for oxygen reduction reaction (ORR). In this study, we established the correlation between the O2 adsorption energy and the electronic structure of transition metal macrocyclic complexes which exhibit activity for ORR. To this end, we have predicted the molecular and electronic structures of a series of transition metal macrocyclic complexes with planar N4 chelation, as well as the molecular and electronic structures for the O2 adsorption on these macrocyclic molecules, using the density functional theory calculation method. We found that the calculated adsorption energy of O2 on the transition metal macrocyclic complexes was linearly related to the average position (relative to the lowest unoccupied molecular orbital of the macrocyclic complexes) of the non-bonding d orbitals (d(z(2)), d(xy), d(xz), and d(yz)) which belong to the central transition metal atom. Importantly, our results suggest that varying the energy level of the non-bonding d orbitals through changing the central transition metal atom and/or peripheral ligand groups could be an effective way to tuning their O2 adsorption energy for enhancing the ORR activity of transition metal macrocyclic complex catalysts.

Studies of electronic structure of ZnO grain boundary and its proximity by using spatially resolved electron energy loss spectroscopy

NASA Astrophysics Data System (ADS)

Ong, H. C.; Dai, J. Y.; Du, G. T.

2002-07-01

The low electron energy loss and complex dielectric functions of an arbitrary grain boundary and its proximity in ZnO thin films have been studied by using the spatially resolved electron energy loss spectroscopy. The critical point parameters have been determined by fitting the dielectric functions simultaneously with analytical line shape model. Gradual changes have been observed in the dielectric functions spectra. The critical points are found to redshift and then blueshift when the electron beam scanned across the grain boundary, which suggest the distinctive electronic structure not only of the grain boundary but also of the depletion region. In addition, comparison has been made between the experiment and the recent theoretical studies to account for the interband transitions that occur in the grain boundaries. Several features predicted by the theory are qualitatively found to be consistent with our results. The presence of dangling bonds instead of bond distortion is attributed to be the major cause of defects in the grain boundaries of ZnO.

Density Functional Study of Structures and Electron Affinities of BrO4F/BrO4F−

PubMed Central

Gong, Liangfa; Xiong, Jieming; Wu, Xinmin; Qi, Chuansong; Li, Wei; Guo, Wenli

2009-01-01

The structures, electron affinities and bond dissociation energies of BrO4F/BrO4F− species have been investigated with five density functional theory (DFT) methods with DZP++ basis sets. The planar F-Br…O2…O2 complexes possess 3A′ electronic state for neutral molecule and 4A′ state for the corresponding anion. Three types of the neutral-anion energy separations are the adiabatic electron affinity (EAad), the vertical electron affinity (EAvert), and the vertical detachment energy (VDE). The EAad value predicted by B3LYP method is 4.52 eV. The bond dissociation energies De (BrO4F → BrO4-mF + Om) (m = 1–4) and De− (BrO4F− → BrO4-mF− + Om and BrO4F− → BrO4-mF + Om−) are predicted. The adiabatic electron affinities (EAad) were predicted to be 4.52 eV for F-Br…O2…O2 (3A′←4A′) (B3LYP method). PMID:19742128

A complete active space valence bond method with nonorthogonal orbitals

NASA Astrophysics Data System (ADS)

Hirao, Kimihiko; Nakano, Haruyuki; Nakayama, Kenichi

1997-12-01

A complete active space self-consistent field (SCF) wave function is transformed into a valence bond type representation built from nonorthogonal orbitals, each strongly localized on a single atom. Nonorthogonal complete active space SCF orbitals are constructed by Ruedenberg's projected localization procedure so that they have maximal overlaps with the corresponding minimum basis set of atomic orbitals of the free-atoms. The valence bond structures which are composed of such nonorthogonal quasiatomic orbitals constitute the wave function closest to the concept of the oldest and most simple valence bond method. The method is applied to benzene, butadiene, hydrogen, and methane molecules and compared to the previously proposed complete active space valence bond approach with orthogonal orbitals. The results demonstrate the validity of the method as a powerful tool for describing the electronic structure of various molecules.

Blue-shifted and red-shifted hydrogen bonds: Theoretical study of the CH3CHO· · ·HNO complexes

NASA Astrophysics Data System (ADS)

Yang, Yong; Zhang, Weijun; Gao, Xiaoming

The blue-shifted and red-shifted H-bonds have been studied in complexes CH3CHO?HNO. At the MP2/6-31G(d), MP2/6-31+G(d,p) MP2/6-311++G(d,p), B3LYP/6-31G(d), B3LYP/6-31+G(d,p) and B3LYP/6-311++G(d,p) levels, the geometric structures and vibrational frequencies of complexes CH3CHO?HNO are calculated by both standard and CP-corrected methods, respectively. Complex A exhibits simultaneously red-shifted C bond H?O and blue-shifted N bond H?O H-bonds. Complex B possesses simultaneously two blue-shifted H-bonds: C bond H?O and N bond H?O. From NBO analysis, it becomes evident that the red-shifted C bond H?O H-bond can be explained on the basis of the two opposite effects: hyperconjugation and rehybridization. The blue-shifted C bond H?O H-bond is a result of conjunct C bond H bond strengthening effects of the hyperconjugation and the rehybridization due to existence of the significant electron density redistribution effect. For the blue-shifted N bond H?O H-bonds, the hyperconjugation is inhibited due to existence of the electron density redistribution effect. The large blue shift of the N bond H stretching frequency is observed because the rehybridization dominates the hyperconjugation.

On the Origin of the Methyl Radical Loss from Deprotonated Ferulic and Isoferulic Acids: Electronic Excitation of a Transient Structure

NASA Astrophysics Data System (ADS)

Zhang, Xiaoping; Li, Fei; Lv, Huiqing; Wu, Yanqing; Bian, Gaofeng; Jiang, Kezhi

2013-06-01

Formation of radical fragments from even-electron ions is an exception to the "even-electron rule". In this work, ferulic acid (FA) and isoferulic acid (IFA) were used as the model compounds to probe the fragmentation mechanisms and the isomeric effects on homolytic cleavage. Elimination of methyl radical and CO2 are the two competing reactions observed in the CID-MS of [FA - H]- and [IFA - H]-, of which losing methyl radical violates the "even-electron rule". The relative intensity of their product ions is significantly different, and thereby the two isomeric compounds can be differentiated by tandem MS. Theoretical calculations indicate that both the singlet-triplet gap and the excitation energy decrease in the transient structures, as the breaking C-O bond is lengthened. The methyl radical elimination has been rationalized as the intramolecular electronic excitation of a transient structure with an elongating C-O bond. The potential energy diagrams, completed by the addition of the energy barrier of the radical elimination, have provided a reasonable explanation of the different CID-MS behaviors of [FA - H]- and [IFA - H]-.

Identification of non-classical C-H···M interactions in early and late transition metal complexes containing the CH(ArO)3 ligand.

PubMed

Lein, Matthias; Harrison, John A; Nielson, Alastair J

2013-08-14

The fully optimised DFT structure of the d(0) complex [{CH(ArO)3}Ti(NEt2)] (2) at the B3LYP level compares well with the distorted tetrahedral geometry shown by the X-ray crystal structure. QTAIM analysis of the electron density associated with the C-H···Ti interaction shows a well defined bond critical point, a bond path between the hydrogen and titanium centres and a negative value for the energy density indicative of covalency. A natural bond orbital (NBO) picture of the interaction shows that the C-H σ bond electron density donates to a d hybrid orbital on the metal in a linear fashion. Calculated IR and NMR data for the components of the interaction are consistent with experiment. The computed structures for [{CH(ArO)3}Ti(OPh)] (3), [{CH(ArO)3}Zr(NEt2)] (4), [{CH(ArO)3}Hf(NEt2)] (5), show tetrahedral geometries and QTAIM and NBO properties similar to (2). [{CH(ArO)3}Mo(NEt2)] (6) shows distortion of the tripodal ligand and a reduced C-H···M bond angle with properties more consistent with a C-H···M side-on donor interaction. In [{CH(ArO)3}Fe(NEt2)] (7) the C-H···M bond angle is linear and involves a donor interaction. An energy minimised structure maintaining the three fold coordination to the tripodal ligand was not obtained for [{CH(ArO)3}Ni(NEt2)](2-) but changing from a diethyl amide ligand to phenolato gave energy minimised [{CH(ArO)3}Ni(OPh)](2-) (8). This structure shows a distorted square planar geometry with a substantially bent phenoxo ligand and a near linear C-H···M covalent interaction with donor and back bonding properties. The work shows that linear C-H···M interactions can have both agostic and weak hydrogen bond-like covalency.

Electronic structure and reactivity of three-coordinate iron complexes.

PubMed

Holland, Patrick L

2008-08-01

[Reaction: see text]. The identity and oxidation state of the metal in a coordination compound are typically thought to be the most important determinants of its reactivity. However, the coordination number (the number of bonds to the metal) can be equally influential. This Account describes iron complexes with a coordination number of only three, which differ greatly from iron complexes with octahedral (six-coordinate) geometries with respect to their magnetism, electronic structure, preference for ligands, and reactivity. Three-coordinate complexes with a trigonal-planar geometry are accessible using bulky, anionic, bidentate ligands (beta-diketiminates) that steer a monodentate ligand into the plane of their two nitrogen donors. This strategy has led to a variety of three-coordinate iron complexes in which iron is in the +1, +2, and +3 oxidation states. Systematic studies on the electronic structures of these complexes have been useful in interpreting their properties. The iron ions are generally high spin, with singly occupied orbitals available for pi interactions with ligands. Trends in sigma-bonding show that iron(II) complexes favor electronegative ligands (O, N donors) over electropositive ligands (hydride). The combination of electrostatic sigma-bonding and the availability of pi-interactions stabilizes iron(II) fluoride and oxo complexes. The same factors destabilize iron(II) hydride complexes, which are reactive enough to add the hydrogen atom to unsaturated organic molecules and to take part in radical reactions. Iron(I) complexes use strong pi-backbonding to transfer charge from iron into coordinated alkynes and N 2, whereas iron(III) accepts charge from a pi-donating imido ligand. Though the imidoiron(III) complex is stabilized by pi-bonding in the trigonal-planar geometry, addition of pyridine as a fourth donor weakens the pi-bonding, which enables abstraction of H atoms from hydrocarbons. The unusual bonding and reactivity patterns of three-coordinate iron compounds may lead to new catalysts for oxidation and reduction reactions and may be used by nature in transient intermediates of nitrogenase enzymes.

Pentaatomic planar tetracoordinate silicon with 14 valence electrons: a large-scale global search of SiX(n)Y(m)(q) (n + m = 4; q = 0, ±1, -2; X, Y = main group elements from H to Br).

PubMed

Xu, Jing; Ding, Yi-hong

2015-03-05

Designing and characterizing the compounds with exotic structures and bonding that seemingly contrast the traditional chemical rules are a never-ending goal. Although the silicon chemistry is dominated by the tetrahedral picture, many examples with the planar tetracoordinate-Si skeletons have been discovered, among which simple species usually contain the 17/18 valence electrons. In this work, we report hitherto the most extensive structural search for the pentaatomic ptSi with 14 valence electrons, that is, SiXnYm(q) (n + m = 4; q = 0, ±1, -2; X, Y = main group elements from H to Br). For 129 studied systems, 50 systems have the ptSi structure as the local minimum. Promisingly, nine systems, that is, Li3SiAs(2-), HSiY3 (Y = Al/Ga), Ca3SiAl(-), Mg4Si(2-), C2LiSi, Si3Y2 (Y = Li/Na/K), each have the global minimum ptSi. The former six systems represent the first prediction. Interestingly, in HSiY3 (Y = Al/Ga), the H-atom is only bonded to the ptSi-center via a localized 2c-2e σ bond. This sharply contradicts the known pentaatomic planar-centered systems, in which the ligands are actively involved in the ligand-ligand bonding besides being bonded to the planar center. Therefore, we proposed here that to generalize the 14e-ptSi, two strategies can be applied as (1) introducing the alkaline/alkaline-earth elements and (2) breaking the peripheral bonding. In light of the very limited global ptSi examples, the presently designed six systems with 14e are expected to enrich the exotic ptSi chemistry and welcome future laboratory confirmation. © 2014 Wiley Periodicals, Inc.

EELS from organic crystalline materials

NASA Astrophysics Data System (ADS)

Brydson, R.; Eddleston, M. D.; Jones, W.; Seabourne, C. R.; Hondow, N.

2014-06-01

We report the use of the electron energy loss spectroscopy (EELS) for providing light element chemical composition information from organic, crystalline pharmaceutical materials including theophylline and paracetamol and discuss how this type of data can complement transmission electron microscopy (TEM) imaging and electron diffraction when investigating polymorphism. We also discuss the potential for the extraction of bonding information using electron loss near-edge structure (ELNES).

Investigation of low-loss spectra and near-edge fine structure of polymers by PEELS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heckmann, W.

Transmission electron microscopy has changed from a purely imaging method to an analytical method. This has been facilitated particularly by equipping electron microscopes with energy filters and with parallel electron energy loss spectrometers (PEELS). Because of their relatively high energy resolution (1 to 2 eV) they provide information not only on the elements present but also on the type of bonds between the molecular groups. Polymers are radiation sensitive and the molecular bonds change as the spectrum is being recorded. This can be observed with PEEL spectrometers that are able to record spectra with high sensitivity and in rapid succession.

Predictive Modeling in Actinide Chemistry and Catalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Ping

2016-05-16

These are slides from a presentation on predictive modeling in actinide chemistry and catalysis. The following topics are covered in these slides: Structures, bonding, and reactivity (bonding can be quantified by optical probes and theory, and electronic structures and reaction mechanisms of actinide complexes); Magnetic resonance properties (transition metal catalysts with multi-nuclear centers, and NMR/EPR parameters); Moving to more complex systems (surface chemistry of nanomaterials, and interactions of ligands with nanoparticles); Path forward and conclusions.

Improved stability of a metallic state in benzothienobenzothiophene-based molecular conductors: an effective increase of dimensionality with hydrogen bonds.

PubMed

Higashino, Toshiki; Ueda, Akira; Yoshida, Junya; Mori, Hatsumi

2017-03-25

A dihydroxy-substituted benzothienobenzothiophene, BTBT(OH) 2 , was synthesized, and its charge-transfer (CT) salt, β-[BTBT(OH) 2 ] 2 ClO 4 , was successfully obtained. Thanks to the introduced hydroxy groups, a hydrogen-bonded chain structure connecting the BTBT molecules and counter anions was formed in the CT salt, which effectively increases the dimensionality of the electronic structure and consequently leads to a stable metallic state.

Comparative structural analysis of cytidine, ethenocytidine and their protonated salts. II. IR spectral studies.

PubMed Central

Krzyzosiak, W; Jaskólski, M; Sierzputowska-Gracz, H; Wiewiórowski, M

1982-01-01

The IR spectra of crystalline cytidine (Cyd), ethenocytidine (epsilon Cyd), and their hydrochlorides (Cyd-Hcl and epsilon CyD-HCl) have been analyzed to determine the spectroscopic manifestations of the structural differences that were previously established for these nucleosides from X-ray studies. O,N-Deuteration of the samples turned out to be a successful approach to obtaining interpretable spectra. The analysis was carried out in three frequency ranges: (i) The 2600-1900 cm-1 range originating from the vO-D and VN-D vibrations. All intermolecular hydrogen bonds could be recognized here. The positions of the individual vO-D (vN-D) bands were correlated with the geometrical delta HB parameters presenting the strengths of hydrogen bonds in which these groups act as donors (ii) The 1750-1500 cm-1 region originating from the stretching vibrations of double bonds. All absorption bands in this region were interpreted in terms of electronic structures of the base fragments. (iii) The region of the C-H stretching vibrations of the base fragments (3200-3000 cm-1) and sugar moieties (3000-2800 cm-1). The Csp2-H vibrations also reflect the electronic structures of the base fragments, whereas the vCsp-H frequencies seem to be sensitive to etheno-bridging and to the presence of an intramolecular C6-H...05' hydrogen bond. PMID:7079184

Sandblasting may damage the surface of composite CAD-CAM blocks.

PubMed

Yoshihara, Kumiko; Nagaoka, Noriyuki; Maruo, Yukinori; Nishigawa, Goro; Irie, Masao; Yoshida, Yasuhiro; Van Meerbeek, Bart

2017-03-01

CAD-CAM blocks to fabricate semi-direct and indirect restorations are available in different sorts of ceramics as well as composite. In order to bond restorations prepared out of composite blocks into tooth cavities, it is recommended to gently sandblast the surface prior to the application of a primer/adhesive. Today, the effect of sandblasting composite block surfaces has not thoroughly been investigated. In this study, the ultra-structure of composite CAD-CAM blocks was investigated with special attention to the effect of sandblasting on the surface topography and of silanization on the bonding performance. Five different composite CAD-CAM blocks were involved. We correlatively investigated their structural and chemical composition using X-ray diffraction (XRD), energy dispersion spectroscopy (EDS), scanning electron microscopy (SEM) and (scanning) transmission electron microscopy ((S)TEM). The effect of sandblasting was also imaged in cross-section and at the interface with composite cement. Finally, we measured the shear bond strength to the sandblasted block surface with and without silanization. All composite blocks revealed a different ultra-structure. Sandblasting increased surface roughness and resulted in an irregular surface with some filler exposure. Sandblasting also damaged the surface. When the sandblasted composite blocks were silanized, superior bonding receptiveness in terms of higher bond strength was achieved except for Shofu Block HC. Sandblasting followed by silanization improved the bond strength to composite CAD-CAM blocks. However, sandblasting may also damage the composite CAD-CAM block surface. For the composite CAD-CAM block Shofu Block HC, the damage was so severe that silanization did not improve bond strength. Copyright © 2016 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Ultrathin silicon oxynitride layer on GaN for dangling-bond-free GaN/insulator interface.

PubMed

Nishio, Kengo; Yayama, Tomoe; Miyazaki, Takehide; Taoka, Noriyuki; Shimizu, Mitsuaki

2018-01-23

Despite the scientific and technological importance of removing interface dangling bonds, even an ideal model of a dangling-bond-free interface between GaN and an insulator has not been known. The formation of an atomically thin ordered buffer layer between crystalline GaN and amorphous SiO 2 would be a key to synthesize a dangling-bond-free GaN/SiO 2 interface. Here, we predict that a silicon oxynitride (Si 4 O 5 N 3 ) layer can epitaxially grow on a GaN(0001) surface without creating dangling bonds at the interface. Our ab initio calculations show that the GaN/Si 4 O 5 N 3 structure is more stable than silicon-oxide-terminated GaN(0001) surfaces. The electronic properties of the GaN/Si 4 O 5 N 3 structure can be tuned by modifying the chemical components near the interface. We also propose a possible approach to experimentally synthesize the GaN/Si 4 O 5 N 3 structure.

Microscopic Electronic and Mechanical Properties of Ultra-Thin Layered Materials

DTIC Science & Technology

2016-07-25

Graphene single layers grown by chemical vapor deposition on single crystal Cu substrates are subject to nonuniform physisorption strains that...the observed highly nonuniform strains. 4. Connecting dopant bond type with electronic structure in N-doped graphene (reference [4]) Robust methods

Photoelectron diffraction from single oriented molecules: Towards ultrafast structure determination of molecules using x-ray free-electron lasers

NASA Astrophysics Data System (ADS)

Kazama, Misato; Fujikawa, Takashi; Kishimoto, Naoki; Mizuno, Tomoya; Adachi, Jun-ichi; Yagishita, Akira

2013-06-01

We provide a molecular structure determination method, based on multiple-scattering x-ray photoelectron diffraction (XPD) calculations. This method is applied to our XPD data on several molecules having different equilibrium geometries. Then it is confirmed that, by our method, bond lengths and bond angles can be determined with a resolution of less than 0.1 Å and 10∘, respectively. Differently from any other scenario of ultrafast structure determination, we measure the two- or three-dimensional XPD of aligned or oriented molecules in the energy range from 100 to 200 eV with a 4π detection velocity map imaging spectrometer. Thanks to the intense and ultrashort pulse properties of x-ray free-electron lasers, our approach exhibits the most probable method for obtaining ultrafast real-time structural information on small to medium-sized molecules consisting of light elements, i.e., a “molecular movie.”

Electronic origin of structural transition in 122 Fe based superconductors

NASA Astrophysics Data System (ADS)

Ghosh, Haranath; Sen, Smritijit; Ghosh, Abyay

2017-03-01

Direct quantitative correlations between the orbital order and orthorhombicity is achieved in a number of Fe-based superconductors of 122 family. The former (orbital order) is calculated from first principles simulations using experimentally determined doping and temperature dependent structural parameters while the latter (the orthorhombicity) is taken from already established experimental studies; when normalized, both the above quantities quantitatively corresponds to each other in terms of their doping as well as temperature variations. This proves that the structural transition in Fe-based materials is electronic in nature due to orbital ordering. An universal correlations among various structural parameters and electronic structure are also obtained. Most remarkable among them is the mapping of two Fe-Fe distances in the low temperature orthorhombic phase, with the band energies Edxz, Edyz of Fe at the high symmetry points of the Brillouin zone. The fractional co-ordinate zAs of As which essentially determines anion height is inversely (directly) proportional to Fe-As bond distances (with exceptions of K doped BaFe2As2) for hole (electron) doped materials as a function of doping. On the other hand, Fe-As bond-distance is found to be inversely (directly) proportional to the density of states at the Fermi level for hole (electron) doped systems. Implications of these results to current issues of Fe based superconductivity are discussed.

Application of I-structure though-glass interconnect filled with submicron gold particles to a hermetic sealing device

NASA Astrophysics Data System (ADS)

Nomura, Kazuya; Okada, Akiko; Shoji, Shuichi; Ogashiwa, Toshinori; Mizuno, Jun

2016-10-01

We propose hermetic sealing of a glass-to-glass structure with an I-structure through-glass interconnect via (TGV) filled with submicron Au particles. The top and bottom bumps and the TGV were formed by a simple filling process with a bump-patterned dry film resist. The sealing devices consisting of two glass substrates were bonded via Au interlayers. Vacuum ultraviolet irradiation in the presence of oxygen gas (VUV/O3) pretreatment was used for low-temperature Au-Au bonding at 200 °C. The bonded samples showed He leakage rates of less than 1.3  ×  10-9 Pa m3 s-1. The cross-sectional scanning electron microscope images of the fabricated I-structure TGV showed perfect adhesion between the I-structure TGV and glass substrate. These results indicate that the proposed I-structure TGV is suitable for hermetic sealing devices.

Polarized XANES Monitors Femtosecond Structural Evolution of Photoexcited Vitamin B 12

DOE PAGES

Miller, Nicholas A.; Deb, Aniruddha; Alonso-Mori, Roberto; ...

2017-01-30

Ultrafast, polarization-selective time-resolved X-ray absorption near-edge structure (XANES) was used to characterize the photochemistry of vitamin B 12, cyanocobalamin (CNCbl), in solution. Cobalamins are important biological cofactors involved in methyl transfer, radical rearrangement, and light-activated gene regulation, while also holding promise as light-activated agents for spatiotemporal controlled delivery of therapeutics. We introduce polarized femtosecond XANES, combined with UV–visible spectroscopy, to reveal sequential structural evolution of CNCbl in the excited electronic state. Femtosecond polarized XANES provides the crucial structural dynamics link between computed potential energy surfaces and optical transient absorption spectroscopy. Polarization selectivity can be used to uniquely identify electronic contributionsmore » and structural changes, even in isotropic samples when well-defined electronic transitions are excited. Our XANES measurements reveal that the structural changes upon photoexcitation occur mainly in the axial direction, where elongation of the axial Co–CN bond and Co–N Im bond on a 110 fs time scale is followed by corrin ring relaxation on a 260 fs time scale. In conclusion, these observations expose features of the potential energy surfaces controlling cobalamin reactivity and deactivation.« less

Polarized XANES Monitors Femtosecond Structural Evolution of Photoexcited Vitamin B 12

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, Nicholas A.; Deb, Aniruddha; Alonso-Mori, Roberto

Ultrafast, polarization-selective time-resolved X-ray absorption near-edge structure (XANES) was used to characterize the photochemistry of vitamin B 12, cyanocobalamin (CNCbl), in solution. Cobalamins are important biological cofactors involved in methyl transfer, radical rearrangement, and light-activated gene regulation, while also holding promise as light-activated agents for spatiotemporal controlled delivery of therapeutics. We introduce polarized femtosecond XANES, combined with UV–visible spectroscopy, to reveal sequential structural evolution of CNCbl in the excited electronic state. Femtosecond polarized XANES provides the crucial structural dynamics link between computed potential energy surfaces and optical transient absorption spectroscopy. Polarization selectivity can be used to uniquely identify electronic contributionsmore » and structural changes, even in isotropic samples when well-defined electronic transitions are excited. Our XANES measurements reveal that the structural changes upon photoexcitation occur mainly in the axial direction, where elongation of the axial Co–CN bond and Co–N Im bond on a 110 fs time scale is followed by corrin ring relaxation on a 260 fs time scale. In conclusion, these observations expose features of the potential energy surfaces controlling cobalamin reactivity and deactivation.« less

Structural and electronic properties for atomic clusters

NASA Astrophysics Data System (ADS)

Sun, Yan

We have studied the structural and electronic properties for different groups of atomic clusters by doing a global search on the potential energy surface using the Taboo Search in Descriptors Space (TSDS) method and calculating the energies with Kohn-Sham Density Functional Theory (KS-DFT). Our goal was to find the structural and electronic principles for predicting the structure and stability of clusters. For Ben (n = 3--20), we have found that the evolution of geometric and electronic properties with size reflects a change in the nature of the bonding from van der Waals to metallic and then bulk-like. The cluster sizes with extra stability agree well with the predictions of the jellium model. In the 4d series of transition metal (TM) clusters, as the d-type bonding becomes more important, the preferred geometric structure changes from icosahedral (Y, Zr), to distorted compact structures (Nb, Mo), and FCC or simple cubic crystal fragments (Tc, Ru, Rh) due to the localized nature of the d-type orbital. Analysis of relative isomer energies and their electronic density of states suggest that these clusters tend to follow a maximum hardness principle (MHP). For A4B12 clusters (A is divalent, B is monovalent), we found unusually large (on average 1.95 eV) HOMO-LUMO gap values. This shows the extra stability at an electronic closed shell (20 electrons) predicted by the jellium model. The importance of symmetry, closed electronic and ionic shells in stability is shown by the relative stability of homotops of Mg4Ag12 which also provides support for the hypothesis that clusters that satisfy more than one stability criterion ("double magic") should be particularly stable.

Chemical Modification of Graphene Oxide by Nitrogenation: An X-ray Absorption and Emission Spectroscopy Study

DOE PAGES

Chuang, Cheng-Hao; Ray, Sekhar C.; Mazumder, Debarati; ...

2017-02-10

Nitrogen-doped graphene oxides (GO:N x) were synthesized by a partial reduction of graphene oxide (GO) using urea [CO(NH 2) 2 ]. Their electronic/bonding structures were investigated using X-ray absorption near-edge structure (XANES), valence-band photoemission spectroscopy (VB-PES), X-ray emission spectroscopy (XES) and resonant inelastic X-ray scattering (RIXS). During GO:N x synthesis, different nitrogen-bonding species, such as pyrrolic/graphitic-nitrogen, were formed by replacing of oxygen-containing functional groups. At lower N-content (2.7 at%), pyrrolic-N, owing to surface and subsurface diffusion of C, N and NH is deduced from various X-ray spectroscopies. In contrast, at higher N-content (5.0 at%) graphitic nitrogen was formed in whichmore » each N-atom trigonally bonds to three distinct sp 2 -hybridized carbons with substitution of the N-atoms for C atoms in the graphite layer. Upon nitrogen substitution, the total density of state close to Fermi level is increased to raise the valence-band maximum, as revealed by VB-PES spectra, indicating an electron donation from nitrogen, molecular bonding C/N/O coordination or/and lattice structure reorganization in GO:N x . The well-ordered chemical environments induced by nitrogen dopant are revealed by XANES and RIXS measurements.« less

Chemical Modification of Graphene Oxide by Nitrogenation: An X-ray Absorption and Emission Spectroscopy Study

NASA Astrophysics Data System (ADS)

Chuang, Cheng-Hao; Ray, Sekhar C.; Mazumder, Debarati; Sharma, Surbhi; Ganguly, Abhijit; Papakonstantinou, Pagona; Chiou, Jau-Wern; Tsai, Huang-Ming; Shiu, Hung-Wei; Chen, Chia-Hao; Lin, Hong-Ji; Guo, Jinghua; Pong, Way-Faung

2017-02-01

Nitrogen-doped graphene oxides (GO:Nx) were synthesized by a partial reduction of graphene oxide (GO) using urea [CO(NH2)2]. Their electronic/bonding structures were investigated using X-ray absorption near-edge structure (XANES), valence-band photoemission spectroscopy (VB-PES), X-ray emission spectroscopy (XES) and resonant inelastic X-ray scattering (RIXS). During GO:Nx synthesis, different nitrogen-bonding species, such as pyrrolic/graphitic-nitrogen, were formed by replacing of oxygen-containing functional groups. At lower N-content (2.7 at%), pyrrolic-N, owing to surface and subsurface diffusion of C, N and NH is deduced from various X-ray spectroscopies. In contrast, at higher N-content (5.0 at%) graphitic nitrogen was formed in which each N-atom trigonally bonds to three distinct sp2-hybridized carbons with substitution of the N-atoms for C atoms in the graphite layer. Upon nitrogen substitution, the total density of state close to Fermi level is increased to raise the valence-band maximum, as revealed by VB-PES spectra, indicating an electron donation from nitrogen, molecular bonding C/N/O coordination or/and lattice structure reorganization in GO:Nx. The well-ordered chemical environments induced by nitrogen dopant are revealed by XANES and RIXS measurements.

Experimental (X-ray, FT-IR and UV-vis spectra) and theoretical methods (DFT study) of (E)-3-methoxy-2-[(p-tolylimino)methyl]phenol.

PubMed

Demircioğlu, Zeynep; Albayrak, Çiğdem; Büyükgüngör, Orhan

2014-07-15

A suitable single crystal of (E)-3-methoxy-2-[(p-tolylimino)methyl]phenol, formulated as C15H15N1O2, reveals that the structure is adopted to its E configuration about the azomethine C=N double bond. The compound adopts a enol-imine tautomeric form with a strong intramolecular O-H⋯N hydrogen bond. The single crystal X-ray diffraction analysis at 296K crystallizes in the monoclinic space group P21/c with a = 13.4791(11) Å, b = 6.8251(3) Å, c = 18.3561(15) Å, α = 90°, β = 129.296(5)°, γ = 90° and Z = 4. Comprehensive theoretical and experimental structural studies on the molecule have been carried out by FT-IR and UV-vis spectrometry. Optimized molecular structure and harmonic vibrational frequencies have been investigated by DFT/B3LYP method with 6-31G(d,p) basis set. Stability of the molecule, hyperconjugative interactions, charge delocalization and intramolecular hydrogen bond has been analyzed by using natural bond orbital (NBO) analysis. Electronic structures were discussed by TD-DFT method and the relocation of the electron density were determined. The energetic behavior of the title compound has been examined in solvent media using polarizable continuum model (PCM). Molecular electrostatic potential (MEP), Mulliken population method and natural population analysis (NPA) have been studied. Nonlinear optical (NLO) properties were also investigated. In addition, frontier molecular orbitals analysis have been performed from the optimized geometry. An ionization potential (I), electron affinity (A), electrophilicity index (ω), chemical potential (μ), electronegativity (χ), hardness (η), and softness (S), have been investigated. Copyright © 2014 Elsevier B.V. All rights reserved.

Ab initio characterization of coupling strength for all types of dangling-bond pairs on the hydrogen-terminated Si(100)-2 × 1 surface

NASA Astrophysics Data System (ADS)

Shaterzadeh-Yazdi, Zahra; Sanders, Barry C.; DiLabio, Gino A.

2018-04-01

Recent work has suggested that coupled silicon dangling bonds sharing an excess electron may serve as building blocks for quantum-cellular-automata cells and quantum computing schemes when constructed on hydrogen-terminated silicon surfaces. In this work, we employ ab initio density-functional theory to examine the details associated with the coupling between two dangling bonds sharing one excess electron and arranged in various configurations on models of phosphorous-doped hydrogen-terminated silicon (100) surfaces. Our results show that the coupling strength depends strongly on the relative orientation of the dangling bonds on the surface and on the separation between them. The orientation of dangling bonds is determined by the anisotropy of the silicon (100) surface, so this feature of the surface is a significant contributing factor to variations in the strength of coupling between dangling bonds. The results demonstrate that simple models for approximating tunneling, such as the Wentzel-Kramer-Brillouin method, which do not incorporate the details of surface structure, are incapable of providing reasonable estimates of tunneling rates between dangling bonds. The results provide guidance to efforts related to the development of dangling-bond based computing elements.

Quantum Mechanical Metric for Internal Cohesion in Cement Crystals

PubMed Central

Dharmawardhana, C. C.; Misra, A.; Ching, Wai-Yim

2014-01-01

Calcium silicate hydrate (CSH) is the main binding phase of Portland cement, the single most important structural material in use worldwide. Due to the complex structure and chemistry of CSH at various length scales, the focus has progressively turned towards its atomic level comprehension. We study electronic structure and bonding of a large subset of the known CSH minerals. Our results reveal a wide range of contributions from each type of bonding, especially hydrogen bonding, which should enable critical analysis of spectroscopic measurements and construction of realistic C-S-H models. We find the total bond order density (TBOD) as the ideal overall metric for assessing crystal cohesion of these complex materials and should replace conventional measures such as Ca:Si ratio. A rarely known orthorhombic phase Suolunite is found to have higher cohesion (TBOD) in comparison to Jennite and Tobermorite, which are considered the backbone of hydrated Portland cement. PMID:25476741

Crystal structure, electronic structure, and photoluminescent properties of SrMoO{sub 4}:Tb{sup 3+} phosphors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Sung Wook; Moon, Byung Kee; Jeong, Jung Hyun, E-mail: jhjeong@pknu.ac.kr

2015-10-15

Highlights: • SrMoO{sub 4}:Tb{sup 3+} phosphor samples were synthesized at different temperatures. • The crystal and electronic structures, and luminescence properties were studied. • The excitation peak shifts to red with increasing the sintering temperature. • The luminescence mechanism of SrMoO{sub 4}:Tb{sup 3+} was suggested. - Abstract: The experimental and theoretical studies of the optical properties of SrMoO{sub 4}:Tb{sup 3+} phosphors were carried out. The structural, optical, and electronical properties of the phosphors were systematically studied. The phosphor samples were crystallized at different temperatures via a sol–gel method. Excitation spectra of SrMoO{sub 4}:Tb{sup 3+} powder samples exhibited gradual red shiftmore » and luminescent intensity changed with increasing the sintering temperature. Such spectral changes depend strongly on the crystallographic properties such as lattice parameters and crystallinity. The shift of the excitation spectra is mainly ascribed to the covalent bond interaction between Mo−O bonds. An energy band model was demonstrated to describe the luminescence mechanism in the material.« less

First-principles calculations on slip system activation in the rock salt structure: electronic origin of ductility in silver chloride

NASA Astrophysics Data System (ADS)

Nakamura, Atsutomo; Ukita, Masaya; Shimoda, Naofumi; Furushima, Yuho; Toyoura, Kazuaki; Matsunaga, Katsuyuki

2017-06-01

First principles calculations were performed to understand an electronic origin of high ductility in silver chloride (AgCl) with the rock salt structure. From calculations of generalised stacking fault energies for different slip systems, it was found that only the {1 1 0}? slip system is favourably activated in sodium chloride (NaCl) with the same rock salt structure, whereas AgCl shows three kinds of possible slip systems along the ? direction on the {0 0 1}, {1 1 0}, and {1 1 1} planes, which is in excellent agreement with experiment. Detailed analyses of the electronic structures across slip planes showed that the more covalent character of bonding of Ag-Cl than Na-Cl tends to make the slip motion energetically favourable. It was also surprising to find out that strong Ag-Ag covalent bonds across the slip plane are formed in the {0 0 1}〈1 1 0〉 slip system in AgCl, which makes it possible to activate the multiple slip systems in AgCl.

Structural and electronic properties of U{sub n}O{sub m} (n=1-3,m=1-3n) clusters: A theoretical study using screened hybrid density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Yu; Liu, Haitao; Zhang, Ping, E-mail: zhang-ping@iapcm.ac.cn

The structural and electronic properties of small uranium oxide clusters U{sub n}O{sub m} (n=1-3, m=1-3n) are systematically studied within the screened hybrid density functional theory. It is found that the formation of U–O–U bondings and isolated U–O bonds are energetically more stable than U–U bondings. As a result, no uranium cores are observed. Through fragmentation studies, we find that the U{sub n}O{sub m} clusters with the m/n ratio between 2 and 2.5 are very stable, hinting that UO{sub 2+x} hyperoxides are energetically stable. Electronically, we find that the O-2p states always distribute in the deep energy range, and the U-5fmore » states always distribute at the two sides of the Fermi level. The U-6d states mainly hybridize with the U-5f states in U-rich clusters, while hybridizing with O-2p states in O-rich clusters. Our work is the first one on the screened hybrid density functional theory level studying the atomic and electronic properties of the actinide oxide clusters.« less

An experimental and theoretical study of a hydrogen-bonded complex: O-phenylenediamine with 2,6-pyridinedicarboxylic acid

NASA Astrophysics Data System (ADS)

Ghasemi, Khaled; Rezvani, Ali Reza; Habibi-Khorassani, Sayyed Mostafa; Shahraki, Mehdi; Shokrollahi, Ardeshir; Moghimi, Abolghasem; Tamandani, Halimeh Kord; Gavahi, Sara

2015-11-01

The hydrogen-bonded complex, [(OPDH)+(dipicH)-.H2O], between o-phenylenediamine (OPD) and 2,6-pyridinedicarboxylic acid (dipicH2) has been characterized in water by the 1H, 13C NMR and IR spectroscopies. The crystal structure showed that the edge to face C-H⋯π and C-O⋯π stacking interactions between the dipicH2 and OPD rings play an extra significant role in the formation of the hydrogen-bonded complex and supported the H-bonding interactions. The proton transfer also investigated theoretically in gas phase and thermodynamic parameters such as ΔH‡, ΔG‡, ΔS‡ were calculated for this process. Moreover, intramolecular hydrogen-bonding interaction has been recognized by calculating the electron density ρ(r) and Laplacian ∇2ρ(r) at the bond critical point (BCP) using Atoms-In-Molecule (AIM) method and also the interaction between electron acceptor (σ*) of OH with the lone pair of the nitrogen atom as an electron donor using Natural Bond Orbital (NBO) analysis. In addition, the protonation constants of dipicH2 and OPD and the equilibrium constants for the dipic-OPD (1:1) proton transfer system were obtained by the potentiometric pH titration method using the Hyperquad 2008 program. The stoichiometry of the proton transfer species in the solution confirmed the solid state result.

Electron spin resonance investigations of /sup 11/B/sup 12/C, /sup 11/B/sup 13/C, and /sup 10/B/sup 12/C in neon, argon, and krypton matrices at 4 K: Comparison with theoretical results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knight L.B. Jr.; Cobranchi, S.T.; Petty, J.T.

1989-01-15

The first spectroscopic study of the diatomic radical BC is reported which confirms previous theoretical predictions of a /sup 4/summation/sup -/ electronic ground state. The nuclear hyperfine interactions (A tensors) obtained for /sup 11/B, /sup 10/B, and /sup 13/C from the electron spin resonance (ESR) measurements are compared with extensive ab initio CI calculations. The BC molecule is one of the first examples of a small high spin radical for such an in-depth experimental--theoretical comparison. The electronic structure of BC obtained from an analysis of the nuclear hyperfine interaction (hfi) is compared to that obtained from a Mulliken-type population analysismore » conducted on a CI wave function which yields A/sub iso/ and A/sub dip/ results in good agreement with the observed values. The BC radical was generated by the laser vaporization of a boron--carbon mixture and trapped in neon, argon, and krypton matrices at 4 K for a complete ESR characterization. The magnetic parameters (MHz) obtained for /sup 11/B/sup 13/C in solid neon are: g/sub parallel/ = 2.0015(3); g/sub perpendicular/ = 2.0020(3); D(zfs) = 1701(2); /sup 11/B: chemically bondA/sub parallel/chemically bond = 100(1); chemically bondA/sub perpendicular/chemically bond = 79(1); /sup 13/C: chemically bondA/sub parallel/chemically bond = 5(2) and chemically bondA/sub perpendicular/chemically bond = 15(1). Based on comparison with the theoretical results, the most likely choice of signs is that all A values are positive.« less

Christopher Chang | NREL

Science.gov Websites

transition metal systems, macromolecular dynamics, comparative chemical bonding analysis, electron transfer . Research Interests Dynamics and control on discrete structures, including excited-state transition metal

Comparison of the One-electron Oxidations of CO-Bridged vs Unbridged Bimetallic Complexes: Electron-transfer Chemistry of Os2Cp2(CO)4 and Os2Cp*2(μ-CO)2(CO)2 (Cp = η5-C5H5, Cp* = η5-C5Me5)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laws, Derek R.; Bullock, R. Morris; Lee, Richmond

The one-electron oxidations of two dimers of half-sandwich osmium carbonyl complexes have been examined by electrochemistry, spectro-electrochemistry, and computational methods. The all-terminal carbonyl complex Os2Cp2(CO)4 (1, Cp = η5-C5H5) undergoes a reversible one-electron anodic reaction at E1/2 = 0.41 V vs ferrocene in CH2Cl2/0.05 M [NBu4][B(C6F5)4], giving a rare example of a metal-metal bonded radical cation unsupported by bridging ligands. The IR spectrum of 1+ is consistent with an approximately 1:1 mixture of anti and gauche structures for the 33 e- radical cation in which it has retained all-terminal bonding of the CO ligands. DFT calculations, including orbital-occupancy-perturbed Mayer bond-ordermore » analyses, show that the HOMOs of anti-1 and gauche-1 are metal-ligand delocalized. Removal of an electron from 1 has very little effect on the Os-Os bond order, accounting for the resistance of 1+ to heterolytic cleavage. The Os-Os bond distance is calculated to decrease by 0.10 Å and 0.06 Å as a consequence of one-electron oxidation of anti-1 and gauche-1, respectively. The CO-bridged complex Os2Cp*2(μ-CO)2(CO)2 (Cp* = η5-C5Me5), trans-2, undergoes a more facile oxidation, E1/2 = - 0.11 V, giving a persistent radical cation shown by solution IR analysis to preserve its bridged-carbonyl structure. However, ESR analysis of frozen solutions of 2+ is interpreted in terms of the presence of two isomers, most likely anti-2+ and trans-2+, at low temperature. Calculations show that the HOMO of trans-2 is highly delocalized over the metal-ligand framework, with the bridging carbonyls accounting for about half of the orbital makeup. The Os-Os bond order again changes very little with removal of an electron, and the Os-Os bond length actually undergoes minor shortening. Calculations suggest that the second isomer of 2+ has both the trans CO-bridged and the anti all-terminal CO structures. DRL and WEG acknowledge the support of the National Science Foundation under grant CHE-0808909. K-WH acknowledges financial support from KAUST. RMB thanks the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Biosciences and Geosciences for support. Pacific Northwest National Laboratory is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. We thank Dr. S. I. Gorelsky for the discussion on the OOP analysis.« less

Ultrafast Independent N-H and N-C Bond Deformation Investigated with Resonant Inelastic X-Ray Scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eckert, Sebastian; Norell, Jesper; Miedema, Piter S.

Here, the femtosecond excited-state dynamics following resonant photoexcitation enable the selective deformation of N-H and N-C chemical bonds in 2-thiopyridone in aqueous solution with optical or X-ray pulses. In combination with multiconfigurational quantum-chemical calculations, the orbital-specific electronic structure and its ultrafast dynamics accessed with resonant inelastic X-ray scattering at the N 1s level using synchrotron radiation and the soft X-ray free-electron laser LCLS provide direct evidence for this controlled photoinduced molecular deformation and its ultrashort timescale.

Ultrafast Independent N-H and N-C Bond Deformation Investigated with Resonant Inelastic X-Ray Scattering

DOE PAGES

Eckert, Sebastian; Norell, Jesper; Miedema, Piter S.; ...

2017-04-04

Here, the femtosecond excited-state dynamics following resonant photoexcitation enable the selective deformation of N-H and N-C chemical bonds in 2-thiopyridone in aqueous solution with optical or X-ray pulses. In combination with multiconfigurational quantum-chemical calculations, the orbital-specific electronic structure and its ultrafast dynamics accessed with resonant inelastic X-ray scattering at the N 1s level using synchrotron radiation and the soft X-ray free-electron laser LCLS provide direct evidence for this controlled photoinduced molecular deformation and its ultrashort timescale.

Complex transition metal hydrides: linear correlation of countercation electronegativity versus T-D bond lengths.

PubMed

Humphries, T D; Sheppard, D A; Buckley, C E

2015-06-30

For homoleptic 18-electron complex hydrides, an inverse linear correlation has been established between the T-deuterium bond length (T = Fe, Co, Ni) and the average electronegativity of the metal countercations. This relationship can be further employed towards aiding structural solutions and predicting physical properties of novel complex transition metal hydrides.

Microstructure of Reaction Zone Formed During Diffusion Bonding of TiAl with Ni/Al Multilayer

NASA Astrophysics Data System (ADS)

Simões, Sónia; Viana, Filomena; Koçak, Mustafa; Ramos, A. Sofia; Vieira, M. Teresa; Vieira, Manuel F.

2012-05-01

In this article, the characterization of the interfacial structure of diffusion bonding a TiAl alloy is presented. The joining surfaces were modified by Ni/Al reactive multilayer deposition as an alternative approach to conventional diffusion bonding. TiAl substrates were coated with alternated Ni and Al nanolayers. The nanolayers were deposited by dc magnetron sputtering with 14 nm of period (bilayer thickness). Joining experiments were performed at 900 °C for 30 and 60 min with a pressure of 5 MPa. Cross sections of the joints were prepared for characterization of their interfaces by scanning electron microscopy (SEM), transmission electron microscopy (TEM), scanning transmission electron microscopy (STEM), high resolution TEM (HRTEM), energy dispersive x-ray spectroscopy (EDS), and electron backscatter diffraction (EBSD). Several intermetallic compounds form at the interface, assuring the bonding of the TiAl. The interface can be divided into three distinct zones: zone 1 exhibits elongated nanograins, very small equiaxed grains are observed in zone 2, while zone 3 has larger equiaxed grains. EBSD analysis reveals that zone 1 corresponds to the intermetallic Al2NiTi and AlNiTi, and zones 2 and 3 to NiAl.

The structure, energetics, and nature of the chemical bonding of phenylthiol adsorbed on the Au(111) surface: implications for density-functional calculations of molecular-electronic conduction.

PubMed

Bilić, Ante; Reimers, Jeffrey R; Hush, Noel S

2005-03-01

The adsorption of phenylthiol on the Au(111) surface is modeled using Perdew and Wang density-functional calculations. Both direct molecular physisorption and dissociative chemisorption via S-H bond cleavage are considered as well as dimerization to form disulfides. For the major observed product, the chemisorbed thiol, an extensive potential-energy surface is produced as a function of both the azimuthal orientation of the adsorbate and the linear translation of the adsorbate through the key fcc, hcp, bridge, and top binding sites. Key structures are characterized, the lowest-energy one being a broad minimum of tilted orientation ranging from the bridge structure halfway towards the fcc one. The vertically oriented threefold binding sites, often assumed to dominate molecular electronics measurements, are identified as transition states at low coverage but become favored in dense monolayers. A similar surface is also produced for chemisorption of phenylthiol on Ag(111); this displays significant qualitative differences, consistent with the qualitatively different observed structures for thiol chemisorption on Ag and Au. Full contours of the minimum potential energy as a function of sulfur translation over the crystal face are described, from which the barrier to diffusion is deduced to be 5.8 kcal mol(-1), indicating that the potential-energy surface has low corrugation. The calculated bond lengths, adsorbate charge and spin density, and the density of electronic states all indicate that, at all sulfur locations, the adsorbate can be regarded as a thiyl species that forms a net single covalent bond to the surface of strength 31 kcal mol(-1). No detectable thiolate character is predicted, however, contrary to experimental results for alkyl thiols that indicate up to 20%-30% thiolate involvement. This effect is attributed to the asymptotic-potential error of all modern density functionals that becomes manifest through a 3-4 eV error in the lineup of the adsorbate and substrate bands. Significant implications are described for density-functional calculations of through-molecule electron transport in molecular electronics.

Roles of conjugated double bonds in electron-donating capacity of sorghum grains

USDA-ARS?s Scientific Manuscript database

Electron-donating and metal ion complexation ability of tannins play key roles as antioxidants and in mold/bird resistance. In this study, rapid, sensitive, and nondestructive fluorescence excitation-emission (EEM) spectrophotometry was utilized to correlate structural attributes of sorghum tannins...

The molecular structure of 4-methylpyridine-N-oxide: Gas-phase electron diffraction and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Belova, Natalya V.; Girichev, Georgiy V.; Kotova, Vitaliya E.; Korolkova, Kseniya A.; Trang, Nguyen Hoang

2018-03-01

The molecular structure of 4-methylpiridine-N-oxide, 4-MePyO, has been studied by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. Both, quantum chemistry and GED analyses resulted in CS molecular symmetry with the planar pyridine ring. Obtained molecular parameters confirm the hyperconjugation in the pyridine ring and the sp2 hybridization concept of the nitrogen and carbon atoms in the ring. The experimental geometric parameters are in a good agreement with the parameters for non-substituted N-oxide and reproduced very closely by DFT calculations. The presence of the electron-donating CH3 substituent in 4-MePyO leads to a decrease of the ipso-angle and to an increase of r(N→O) in comparison with the non-substituted PyO. Electron density distribution analysis has been performed in terms of natural bond orbitals (NBO) scheme. The nature of the semipolar N→O bond is discussed.

Role of Boron Element on the Electronic Properties of α-Nb5Si3: A First-Principle Study

NASA Astrophysics Data System (ADS)

Pan, Yong; Lin, Yuanhua

2018-03-01

Transition metal silicides (TMSis) are attracting increasing interest from the microelectronics and nanoelectronic industries. In this paper, we use the first-principles method to investigate the B-doped mechanism and the influence of B on the electronic properties of α-Nb5Si3. The calculated results show that B-doped Nb5Si3 is thermodynamically stable at the ground state. The calculated electronic structure shows that the thermodynamically stable B-doped Nb5Si3 is attributed to the 3D-network B-Si bonds and B-Nb bond. In particular, B element prefers to occupy B -IT4 site in comparison to other sites. Moreover, the calculated band structure indicates that Nb5Si3 exhibits metallic behavior at the ground state. We find that B-doping can improve charge overlap between conduction band and the valence band, which effectively improves the electronic properties of Nb5Si3.

Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dr. Asok K. Ray

2012-05-22

During the past decades, considerable theoretical efforts have been devoted to studying the electronic and geometric structures and related properties of surfaces. Such efforts are particularly important for systems like the actinides for which experimental work is relatively difficult to perform due to material problems and toxicity. The actinides are characterized by a gradual filling of the 5f-electron shell with the degree of localization increasing with the atomic number Z along the last series of the periodic table. The open shell of the 5f electrons determines the atomic, molecular, and solid state properties of the actinide elements and their compoundsmore » and understanding the quantum mechanics of the 5f electrons is the defining issue in the chemistry and physics of actinide elements. These elements are also characterized by the increasing prominence of relativistic effects and their studies can, in fact, help us understand the role of relativity throughout the periodic table. However, the electronic and geometric structures of the actinides, specifically the trans-uranium actinides and the roles of the 5f electrons in chemical bonding are still not well understood. This is crucial not only for our understanding of the actinides but also for the fact that the actinides constitute 'the missing link' between the d transition elements and the lanthanides. The 5f orbitals have properties intermediate between those of localized 4f and delocalized 3d orbitals. Thus, a proper understanding of the actinides will help us understand the behavior of the lanthanides and transition metals as well. In fact, there is an urgent need for continued extensive and detailed theoretical research in this area to provide significant and deep understandings of the electronic and geometric structures of the actinides. In this work, we have performed electronic structure studies for plutonium (Pu), americium (Am), and curium (Cm) surfaces, and molecular adsorptions on Pu and Am surfaces. In particular, the region at the boundary of Pu and Am, is widely believed to be the crossover region between d-like itinerant and f-like localized behavior The eventual goal is a complete understanding of the surface chemistry and physics processes of all actinide surfaces, defining the chemistry and physics of such heavy elements. Among the actinides, plutonium, with five 5f electrons in the solid state, is arguably the most complex, fascinating, and enigmatic element known to mankind and has attracted extraordinary scientific and technological interests because of its unique properties, generating a significant body of research in diverse areas, including superconductivity. Pu has, at least, six stable allotropes between room temperature and melting at atmospheric pressure, indicating that the valence electrons can hybridize into a number of complex bonding arrangements. Central and critical questions relate to the electronic structure, localization of the 5f electrons and the magnetism of Pu. For the light-actinides, from Th to Pu, the 5f electrons are believed to be delocalized, hybridizing with the 6d and 7s electrons. For the heavier actinides, Am and beyond, the 5f electrons are localized with the 5f orbitals progressively lower in energy relative to the 6d configuration. Hence, Pu is in a position where the 5f electronic behavior changes from itinerant to localized. As far as magnetism is concerned, a majority of the theoretical calculations continues to claim the existence of magnetism while almost all the experimental results do not find any support for such claims. The second element of interest to us, namely americium, occupies a central position in the actinide series with respect to the involvement of 5f electrons in metallic bonding. It is widely believed that the 5f electrons in Am are localized and that Am undergoes a series of crystallographic phase changes with pressure. Fully-relativistic all electron surface studies of the different phases of Am, initially for the dhcp and the fcc surfaces, can and have provided us with valuable information about chemical bonding in Am and the transitions from f-electron delocalization to f-electron localization in trans-uranium compounds. In particular, a comparative study of the electronic structures of the Pu and Am surfaces using the techniques of all-electron modern density functional theory and beyond can provide significant information about the role of 5f electrons in bond formation as also the localization of the 5f electrons, matters of considerable controversies. The change from metallic 5f bonding into local-moment nonbonding configurations that takes place between Pu and Am is rather unique in the periodic table and is at the very heart of our understanding of electronic structure. We believe that, considering the narrow bandwidth of surface states, any transition from itinerant to localized behavior first takes place at the actinide surfaces with possible reconstructions.« less

Surface Structure and Surface Electronic States Related to Plasma Cleaning of Silicon and Germanium

NASA Astrophysics Data System (ADS)

Cho, Jaewon

This thesis discusses the surface structure and the surface electronic states of Si and Ge(100) surfaces as well as the effects of oxidation process on the silicon oxide/Si(100) interface structure. The H-plasma exposure was performed in situ at low temperatures. The active species, produced in the H-plasma by the rf-excitation of H_2 gas, not only remove microcontaminants such as oxygen and carbon from the surface, but also passivate the surface with atomic hydrogen by satisfying the dangling bonds of the surface atoms. The surfaces were characterized by Angle Resolved UV-Photoemission Spectroscopy (ARUPS) and Low Energy Electron Diffraction (LEED). In the case of Si(100), H-plasma exposure produced ordered H-terminated crystallographic structures with either a 2 x 1 or 1 x 1 LEED pattern. The hydride phases, found on the surfaces of the cleaned Si(100), were shown to depend on the temperature of the surface during H-plasma cleaning. The electronic states for the monohydride and dihydride phases were identified by ARUPS. When the plasma cleaned surface was annealed, the phase transition from the dihydride to monohydride was observed. The monohydride Si-H surface bond was stable up to 460^circC, and the dangling bond surface states were identified after annealing at 500^circC which was accompanied by the spectral shift. The H-terminated surface were characterized to have a flat band structure. For the Ge(100) surface, an ordered 2 x 1 monohydride phase was obtained from the surface cleaned at 180 ^circC. After plasma exposure at <=170^circC a 1 x 1 surface was observed, but the ARUPS indicated that the surface was predominantly composed of disordered monohydride structures. After annealing above the H-dissociation temperatures, the shift in the spectrum was shown to occur with the dangling bond surface states. The H-terminated surfaces were identified to be unpinned. The interface structure of silicon oxide/Si(100) was studied using ARUPS. Spectral shifts were observed, which were dependent on the processes of surface preparation and oxidation. The shift was characterized in association with the band bending. The origins of the spectral shifts were discussed, including defects at interface and H-passivation in Si. The interface structure is considered to be dependent on the surface preparation and oxidation process.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chuvashova, Irina, E-mail: irina.chuvashova@gmail.com; Bayerisches Geoinstitut, University of Bayreuth, D-95440 Bayreuth; Bykova, Elena

In the present study single crystals of rhombohedral α-B were investigated under pressure to 60 GPa by means of single-crystal X-ray diffraction. The bulk modulus of α-B was found to be K=224(7) GPa (K′=3.0(3)). Measurements of interatomic distances as a function of pressure revealed that the intericosahedral two-center two-electron (2c–2e) bonds are almost as stiff as some of intraicosahedral ones. The three-center two-electron (3c–2e) intericosahedral bonds show much higher compliance compared to other bonds in α-B. The vibrational properties of α-B under pressure were investigated by Raman spectroscopy at pressures up to 160 GPa and IR spectroscopy at pressures upmore » to 53 GPa. - Graphical abstract: The rhombohedral α-B is highly incompressible and extremely stable: it maintains its crystal structure up to 160 GPa and its intericosahedral 2e2c bonds are almost as stiff as some of intraicosahedral ones. - Highlights: • Structural stability of α-B has been investigated up to 160 GPa on single crystals. • Single-crystal x-ray diffraction reveals that α-B is highly incompressible. • Compressibility of B{sub 12} icosahedra is considerably lower than that of the bulk material. • Intericosahedral 2e2c bonds are almost as stiff as some of intraicosahedral ones.« less

Na(23)K(9)Tl(15.3): An Unusual Zintl Compound Containing Apparent Tl(5)(7)(-), Tl(4)(8)(-), Tl(3)(7)(-), and Tl(5)(-) Anions.

PubMed

Dong, Zhen-Chao; Corbett, John D.

1996-05-22

Reaction of the neat elements in tantalum containers at 400 degrees C and then 150 degrees C gives the pure title phase. X-ray crystallography shows that the hexagonal structure (P6(3)/mmc, Z = 2, a = 11.235(1) Å, b = 30.133(5) Å) contains relatively high symmetry clusters Tl(5)(7)(-) (D(3)(h)()), Tl(4)(8)(-) (C(3)(v)(), approximately T(d)), and the new Tl(3)(7)(-) (D(infinity)(h)()) plus Tl(5)(-), the last two disordered over the same elongated site in 1:2 proportions. Cation solvation of these anions is tight and specific, providing good Coulombic trapping of weakly bound electrons on the isolated cluster anions. The observed disorder makes the compound structurally a Zintl phase with a closed shell electron count. EHMO calculations on the novel Tl(3)(7)(-) reveal some bonding similarities with the isoelectronic CO(2), with two good sigma(s,p) bonding and two weakly bonding pi MO's. The Tl-Tl bond lengths therein (3.14 Å) are evidently consistent with multiple bonding. The weak temperature-independent paramagnetism and metallic conductivity (rho(293) approximately 90 &mgr;Omega.cm) of the phase are discussed.

Structural and electronic properties of extremely long perylene bisimide nanofibers formed through a stoichiometrically mismatched, hydrogen-bonded complexation.

PubMed

Yagai, Shiki; Seki, Tomohiro; Murayama, Haruno; Wakikawa, Yusuke; Ikoma, Tadaaki; Kikkawa, Yoshihiro; Karatsu, Takashi; Kitamura, Akihide; Honsho, Yoshihito; Seki, Shu

2010-12-06

Extremely long nanofibers, whose lengths reach the millimeter regime, are generated via co-aggregation of a melamine-appended perylene bisimide semiconductor and a substituted cyanurate, both of which are ditopic triple-hydrogen-bonding building blocks; they co-aggregate in an unexpected stoichiometrically mismatched 1:2 ratio. Various microscopic and X-ray diffraction studies suggest that hydrogen-bonded polymeric chains are formed along the long axis of the nanofibers by the 1:2 complexation of the two components, which further stack along the short axis of the nanofibers. The photocarrier generation mechanism in the nanofibers is investigated by time-of-flight (TOF) experiments under electric and magnetic fields, revealing the birth and efficient recombination of singlet geminate electron-hole pairs. Flash-photolysis time-resolved microwave conductivity (FP-TRMC) measurements revealed intrinsic 1D electron mobilities up to 0.6 cm(2) V(-1) s(-1) within nanofibers.

Stretchable electronics based on Ag-PDMS composites

PubMed Central

Larmagnac, Alexandre; Eggenberger, Samuel; Janossy, Hanna; Vörös, Janos

2014-01-01

Patterned structures of flexible, stretchable, electrically conductive materials on soft substrates could lead to novel electronic devices with unique mechanical properties allowing them to bend, fold, stretch or conform to their environment. For the last decade, research on improving the stretchability of circuits on elastomeric substrates has made significant progresses but designing printed circuit assemblies on elastomers remains challenging. Here we present a simple, cost-effective, cleanroom-free process to produce large scale soft electronic hardware where standard surface-mounted electrical components were directly bonded onto all-elastomeric printed circuit boards, or soft PCBs. Ag-PDMS tracks were stencil printed onto a PDMS substrate and soft PCBs were made by bonding the top and bottom layers together and filling punched holes with Ag-PDMS to create vias. Silver epoxy was used to bond commercial electrical components and no mechanical failure was observed after hundreds of stretching cycles. We also demonstrate the fabrication of a stretchable clock generator. PMID:25434843

Carbohydrate–Aromatic Interactions in Proteins

PubMed Central

2015-01-01

Protein–carbohydrate interactions play pivotal roles in health and disease. However, defining and manipulating these interactions has been hindered by an incomplete understanding of the underlying fundamental forces. To elucidate common and discriminating features in carbohydrate recognition, we have analyzed quantitatively X-ray crystal structures of proteins with noncovalently bound carbohydrates. Within the carbohydrate-binding pockets, aliphatic hydrophobic residues are disfavored, whereas aromatic side chains are enriched. The greatest preference is for tryptophan with an increased prevalence of 9-fold. Variations in the spatial orientation of amino acids around different monosaccharides indicate specific carbohydrate C–H bonds interact preferentially with aromatic residues. These preferences are consistent with the electronic properties of both the carbohydrate C–H bonds and the aromatic residues. Those carbohydrates that present patches of electropositive saccharide C–H bonds engage more often in CH−π interactions involving electron-rich aromatic partners. These electronic effects are also manifested when carbohydrate–aromatic interactions are monitored in solution: NMR analysis indicates that indole favorably binds to electron-poor C–H bonds of model carbohydrates, and a clear linear free energy relationships with substituted indoles supports the importance of complementary electronic effects in driving protein–carbohydrate interactions. Together, our data indicate that electrostatic and electronic complementarity between carbohydrates and aromatic residues play key roles in driving protein–carbohydrate complexation. Moreover, these weak noncovalent interactions influence which saccharide residues bind to proteins, and how they are positioned within carbohydrate-binding sites. PMID:26561965

Carbohydrate-Aromatic Interactions in Proteins.

PubMed

Hudson, Kieran L; Bartlett, Gail J; Diehl, Roger C; Agirre, Jon; Gallagher, Timothy; Kiessling, Laura L; Woolfson, Derek N

2015-12-09

Protein-carbohydrate interactions play pivotal roles in health and disease. However, defining and manipulating these interactions has been hindered by an incomplete understanding of the underlying fundamental forces. To elucidate common and discriminating features in carbohydrate recognition, we have analyzed quantitatively X-ray crystal structures of proteins with noncovalently bound carbohydrates. Within the carbohydrate-binding pockets, aliphatic hydrophobic residues are disfavored, whereas aromatic side chains are enriched. The greatest preference is for tryptophan with an increased prevalence of 9-fold. Variations in the spatial orientation of amino acids around different monosaccharides indicate specific carbohydrate C-H bonds interact preferentially with aromatic residues. These preferences are consistent with the electronic properties of both the carbohydrate C-H bonds and the aromatic residues. Those carbohydrates that present patches of electropositive saccharide C-H bonds engage more often in CH-π interactions involving electron-rich aromatic partners. These electronic effects are also manifested when carbohydrate-aromatic interactions are monitored in solution: NMR analysis indicates that indole favorably binds to electron-poor C-H bonds of model carbohydrates, and a clear linear free energy relationships with substituted indoles supports the importance of complementary electronic effects in driving protein-carbohydrate interactions. Together, our data indicate that electrostatic and electronic complementarity between carbohydrates and aromatic residues play key roles in driving protein-carbohydrate complexation. Moreover, these weak noncovalent interactions influence which saccharide residues bind to proteins, and how they are positioned within carbohydrate-binding sites.

Electronic Structure in Pi Systems: Part I. Huckel Theory with Electron Repulsion.

ERIC Educational Resources Information Center

Fox, Marye Anne; Matsen, F. A.

1985-01-01

Pi-CI theory is a simple, semi-empirical procedure which (like Huckel theory) treats pi and pseudo-pi orbitals; in addition, electron repulsion is explicitly included and molecular configurations are mixed. Results obtained from application of pi-CI to ethylene are superior to either the Huckel molecular orbital or valence bond theories. (JN)

Characterizing Bonding Patterns in Diradicals and Triradicals by Density-Based Wave Function Analysis: A Uniform Approach.

PubMed

Orms, Natalie; Rehn, Dirk R; Dreuw, Andreas; Krylov, Anna I

2018-02-13

Density-based wave function analysis enables unambiguous comparisons of the electronic structure computed by different methods and removes ambiguity of orbital choices. We use this tool to investigate the performance of different spin-flip methods for several prototypical diradicals and triradicals. In contrast to previous calibration studies that focused on energy gaps between high- and low spin-states, we focus on the properties of the underlying wave functions, such as the number of effectively unpaired electrons. Comparison of different density functional and wave function theory results provides insight into the performance of the different methods when applied to strongly correlated systems such as polyradicals. We show that canonical molecular orbitals for species like large copper-containing diradicals fail to correctly represent the underlying electronic structure due to highly non-Koopmans character, while density-based analysis of the same wave function delivers a clear picture of the bonding pattern.

Electronic and structural properties of micro-and nanometre-sized crystalline copper monoxide ceramics investigated by positron annihilation

NASA Astrophysics Data System (ADS)

Druzhkov, A. P.; Gizhevskii, B. A.; Arbuzov, V. L.; Kozlov, E. A.; Shalnov, K. V.; Naumov, S. V.; Perminov, D. A.

2002-09-01

Electronic and structural properties of copper monoxide (CuO) sintered as a common ceramic and nanoceramic are studied by positron annihilation spectroscopy. A CuO nanoceramic with crystallite size ranging from 15 to 90 nm was prepared from a common one by shock-wave loading. It is found that the momentum distribution of valence electrons in CuO is shifted, as compared with metallic copper, towards higher momentum values. This result is related to the effect of the Cu 3d-O 2p hybridization in the Cu-O ionic covalent bond formation. It is found that open volumes, identified mainly as small agglomerates of oxygen vacancies, appear at the nanoceramic crystallite interfaces. The degree of the Cu-O bond covalency decreases locally at the crystallite interfaces because of an oxygen deficit. The nanocrystalline state in CuO is shown to be thermally stable up to 700 K.

Structure of Ordinary Ice Ih. Part 1: Ideal Structure of Ice

DTIC Science & Technology

1993-10-01

T., H . Onuki and R. Onaka (1977) Electronic structures of water and ice. Journal of the Physics Society of Japan, 42: 152-158. Shimaoka, K. (1960...nearest neighbors .................................................................................................................. 5 6. H -bond...8 12. Positions of oxygen atoms in the ice % h crystal

{bold {ital Ab initio}} studies of the structural and electronic properties of solid cubane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richardson, S.L.; Martins, J.L.

1998-12-01

In this paper, we report {ital ab initio} calculation of the structural and electronic properties of solid cubane (s-C{sub 8}H{sub 8}) in the local-density approximation. By using an {ital ab initio} constant pressure extended molecular dynamics method with variable cell shape proposed by Wentzcovitch, Martins, and Price, we compute a lattice parameter {ital a} and a bond angle {alpha} for the rhombohedral Bravais lattice and compare it with experimental x-ray data. We obtain bond lengths for the mononuclear C{sub 8}H{sub 8} unit of basis atoms, as well as a density of states and heat of formation. {copyright} {ital 1998} {italmore » The American Physical Society}« less

Electronic structures of AlMoO(y)(-) (y = 1-4) determined by photoelectron spectroscopy and density functional theory calculations.

PubMed

Waller, Sarah E; Mann, Jennifer E; Hossain, Ekram; Troyer, Mary; Jarrold, Caroline C

2012-07-14

Vibrationally-resolved photoelectron spectra of AlMoO(y)(-) (y = 1-4) are presented and analyzed in conjunction with density functional theory computational results. The structures determined for the AlMoO(y) anion and neutral clusters suggest ionic bonding between Al(+) and a MoO(y)(-) or MoO(y)(-2) moiety, and point to the relative stability of Mo=O versus Al=O bonds. The highest occupied and partially occupied orbitals in the anions and neutrals can be described as Mo atomic-like orbitals, so while the Mo is in a higher oxidation state than Al, the most energetically accessible electrons are localized on the molybdenum center.

The water dimer II: Theoretical investigations

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Anamika; Xantheas, Sotiris S.; Saykally, Richard J.

2018-05-01

As the archetype of aqueous hydrogen bonding, the water dimer has been extensively studied by both theory and experiment for nearly seven decades. In this article, we present a detailed chronological review of the theoretical advances made using electronic structure methods to address the structure, hydrogen bonding and vibrational spectroscopy of the water dimer, as well as the role of its potential energy surface in the development of classical force fields to describe intermolecular interactions in clusters and the condensed phases of water.

The Water Dimer II: Theoretical Investigations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukhopadhyay, Anamika; Xantheas, Sotiris S.; Saykally, Richard J.

As the archetype of aqueous hydrogen bonding, the water dimer has been extensively studied by both theory and experiment for nearly seven decades. Here in this article, we present a detailed chronological review of the theoretical advances made using electronic structure methods to address the structure, hydrogen bonding and vibrational spectroscopy of the water dimer, as well as the role of its potential energy surface in the development of classical force fields to describe intermolecular interaction in clusters and the condensed phases of water.

The Water Dimer II: Theoretical Investigations

DOE PAGES

Mukhopadhyay, Anamika; Xantheas, Sotiris S.; Saykally, Richard J.

2018-03-29

As the archetype of aqueous hydrogen bonding, the water dimer has been extensively studied by both theory and experiment for nearly seven decades. Here in this article, we present a detailed chronological review of the theoretical advances made using electronic structure methods to address the structure, hydrogen bonding and vibrational spectroscopy of the water dimer, as well as the role of its potential energy surface in the development of classical force fields to describe intermolecular interaction in clusters and the condensed phases of water.

The electronic structure of oriented poly[2-methoxy-5-(2'-ethyl-hexyloxy)- 1,4-phenylene-vinylene

NASA Astrophysics Data System (ADS)

Chambers, D. K.; Karanam, S.; Qi, D.; Selmic, S.; Losovyj, Y. B.; Rosa, L. G.; Dowben, P. A.

2005-02-01

Poly[2-methoxy-5-(2’-ethyl-hexyloxy)-1,4-phenylene-vinylene] (MEH-PPV) adopts a preferential orientation on indium tin oxide. Although the basic building block of this polymer provides a negligible overall point-group symmetry, the polymer MEH-PPV packs with sufficient order to exhibit band structure. The polymer is fragile with bond cleavage evident following both argon-ion impact and ultraviolet radiation, but annealing leads to the restoration of much of the bond order.

Electron-Transfer-Enhanced Cation-Cation Interactions in Homo- and Heterobimetallic Actinide Complexes: A Relativistic Density Functional Theory Study.

PubMed

Zheng, Ming; Chen, Fang-Yuan; Tian, Jia-Nan; Pan, Qing-Jiang

2018-04-02

To provide deep insight into cation-cation interactions (CCIs) involving hexavalent actinyl species that are major components in spent nuclear fuel and pose important implications for the effective removal of radiotoxic pollutants in the environment, a series of homo- and heterobimetallic actinide complexes supported by cyclopentadienyl (Cp) and polypyrrolic macrocycle (H 4 L) ligands were systematically investigated using relativistic density functional theory. The metal sort in both parts of (THF)(H 2 L)(OAn VI O) and (An') III Cp 3 from U to Np to Pu, as well as the substituent bonding to Cp from electron-donating Me to H to electron-withdrawing Cl, SiH 3 , and SiMe 3 , was changed. Over 0.70 electrons are unraveled to transfer from the electron-rich U III to the electron-deficient An VI of the actinyl moiety, leading to a more stable An V -U IV isomer; in contrast, uranylneptunium and uranylplutonium complexes behave as electron-resonance structures between VI-III and V-IV. These were further corroborated by geometrical and electronic structures. The energies of CCIs (i.e., O exo -An' bonds) were calculated to be -19.6 to -41.2 kcal/mol, affording those of OUO-Np (-23.9 kcal/mol) and OUO-Pu (-19.6 kcal/mol) with less electron transfer (ET) right at the low limit. Topological analyses of the electron density at the O exo -An' bond critical points demonstrate that the CCIs are ET or dative bonds in nature. A positive correlation has been built between the CCIs' strength and corresponding ET amount. It is concluded that the CCIs of O exo -An' are driven by the electrostatic attraction between the actinyl oxo atom (negative) and the actinide ion (positive) and enhanced by their ET. Finally, experimental syntheses of (THF)(H 2 L)(OU VI O)(An') III Cp 3 (An' = U and Np) were well reproduced by thermodynamic calculations that yielded negative free energies in a tetrahydrofuran solution but a positive one for their uranylplutonium analogue, which was synthetically inaccessible. So, our thermodynamics would provide implications for the synthetic possibility of other theoretically designed bimetallic actinide complexes.

A density functional study of second-row dicarbides C2X (X = Na-Cl) with carbon monosulfide molecule: molecular structure and bonding mechanism

NASA Astrophysics Data System (ADS)

Parida, Saroj K.; Sahu, Sridhar

2018-05-01

In present work, a systematic study regarding molecular structure, and bonding mechanism of carbon monosulfide (CS) on second-row dicarbides C2X with (X = Na-Cl) has been investigated within the framework of density functional theory (DFT). In presence of carbon monosulfide molecule, the structures of C2Na, C2Mg, C2Al, and C2Si are found be changed from cyclic to linear, whereas geometries of C2P, C2S, and C2Cl clusters are almost remain unchanged. Interestingly, the bare carbon monosulfide molecule is attached with carbon site of bare C2X clusters rather than the second-row elements (X = Na-Cl). Furthermore, the nature of bonding in C2XCS clusters has been studiedthrough Bader's topological analysis of the electron charge density distribution ρ(r), Laplacian ∇2 ρ(r) and total energy density H BCP at the bond critical points (BCPs) of the clusters within the framework of the atoms in molecules theory (AIM). In C2XCS clusters, electron density at the bond critical point ρ(r) > 0.30 a.u. with negative values of Laplacian ∇2 ρ(r) indicates shared-kind of interactions between both the carbon atoms of C2X and CS molecule. In addition, we also analyze IR spectra that could assist for the experimental detection.

X-ray photoelectron spectrum and electronic properties of a noncentrosymmetric chalcopyrite compound HgGa(2)S(4): LDA, GGA, and EV-GGA.

PubMed

Reshak, Ali Hussain; Khenata, R; Kityk, I V; Plucinski, K J; Auluck, S

2009-04-30

An all electron full potential linearized augmented plane wave method has been applied for a theoretical study of the band structure, density of states, and electron charge density of a noncentrosymmetric chalcopyrite compound HgGa(2)S(4) using three different approximations for the exchange correlation potential. Our calculations show that the valence band maximum (VBM) and conduction band minimum (CBM) are located at Gamma resulting in a direct energy gap of about 2.0, 2.2, and 2.8 eV for local density approximation (LDA), generalized gradient approximation (GGA), and Engel-Vosko (EVGGA) compared to the experimental value of 2.84 eV. We notice that EVGGA shows excellent agreement with the experimental data. This agreement is attributed to the fact that the Engel-Vosko GGA formalism optimizes the corresponding potential for band structure calculations. We make a detailed comparison of the density of states deduced from the X-ray photoelectron spectra with our calculations. We find that there is a strong covalent bond between the Hg and S atoms and Ga and S atoms. The Hg-Hg, Ga-Ga, and S-S bonds are found to be weaker than the Hg-S and Ga-S bonds showing that a covalent bond exists between Hg and S atoms and Ga and S atoms.

Communication: Electronic flux induced by crossing the transition state

NASA Astrophysics Data System (ADS)

Jia, Dongming; Manz, Jörn; Yang, Yonggang

2018-01-01

We present a new effect of chemical reactions, e.g., isomerizations, that occurs when the reactants pass along the transition state, on the way to products. It is based on the well-known fact that at the transition state, the electronic structure of one isomer changes to the other. We discover that this switch of electronic structure causes a strong electronic flux that is well distinguishable from the usual flux of electrons that travel with the nuclei. As a simple but clear example, the effect is demonstrated here for bond length isomerization of Na2 (21Σu+), with adiabatic crossing the barrier between the inner and outer wells of the double minimum potential that support different "Rydberg" and "ionic" type electronic structures, respectively.

Work function tuning at Au-HfO{sub 2} interfaces using organophosphonate monolayers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwan, Matthew; Cardinal, Thomas; Ramanath, Ganpati, E-mail: Ramanath@rpi.edu

2016-05-09

We show that introducing organophosphonate nanomolecular monolayers (NMLs) at Au-HfO{sub 2} interfaces shift the effective work function by 0.2 eV ≥ ΔΦ{sub eff} ≥ −0.6 eV, due to NML body and bonding dipoles. Electron spectroscopy of NML-Au, NML-HfO{sub 2,} and Au-NML-HfO{sub 2} structures indicate that the Au-NML bond strength is the major factor. Au-NML covalent bonding yields ΔΦ{sub eff} ∼ − 0.2 eV, while weak bonding yields ΔΦ{sub eff} ∼ 0.6 eV. In contrast, NMLs on HfO{sub 2} decrease Φ{sub eff} by ∼0.4 eV due to competing contributions from NML-HfO{sub 2} bonding strength and NML orientation. These findings are relevant for nanomolecularly tailoring the electronic properties of metal–ceramic interfaces for applications.

AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid Sb from 913 K to 1193 K

NASA Astrophysics Data System (ADS)

Hao, Qing-Hai; Li, Y. D.; Kong, Xiang-Shan; Liu, C. S.

2013-02-01

Ab initio molecular dynamics simulations on liquid Sb have been carried out at five different temperatures from 913 K to 1193 K. We have investigated the temperature dependence of structure properties including structural factor S(Q), pair correlation function g(r), bond-angle distribution function g3(θ), cluster properties and bond order parameter Q4 and Q6. A shoulder was reproduced in the high wave number side of the first peak in the S(Q) implying that the residual structure units of crystalline Sb remain in liquid Sb. There is a noticeable bend at around 1023 K in the temperature dependence of the first-peak height of S(Q), the cluster properties and bond order parameter Q4, respectively, indicating that an abnormal structural change may occur at 973-1023 K.

Observation of an all-boron fullerene

NASA Astrophysics Data System (ADS)

Zhai, Hua-Jin; Zhao, Ya-Fan; Li, Wei-Li; Chen, Qiang; Bai, Hui; Hu, Han-Shi; Piazza, Zachary A.; Tian, Wen-Juan; Lu, Hai-Gang; Wu, Yan-Bo; Mu, Yue-Wen; Wei, Guang-Feng; Liu, Zhi-Pan; Li, Jun; Li, Si-Dian; Wang, Lai-Sheng

2014-08-01

After the discovery of fullerene-C60, it took almost two decades for the possibility of boron-based fullerene structures to be considered. So far, there has been no experimental evidence for these nanostructures, in spite of the progress made in theoretical investigations of their structure and bonding. Here we report the observation, by photoelectron spectroscopy, of an all-boron fullerene-like cage cluster at B40- with an extremely low electron-binding energy. Theoretical calculations show that this arises from a cage structure with a large energy gap, but that a quasi-planar isomer of B40- with two adjacent hexagonal holes is slightly more stable than the fullerene structure. In contrast, for neutral B40 the fullerene-like cage is calculated to be the most stable structure. The surface of the all-boron fullerene, bonded uniformly via delocalized σ and π bonds, is not perfectly smooth and exhibits unusual heptagonal faces, in contrast to C60 fullerene.

Observation of an all-boron fullerene.

PubMed

Zhai, Hua-Jin; Zhao, Ya-Fan; Li, Wei-Li; Chen, Qiang; Bai, Hui; Hu, Han-Shi; Piazza, Zachary A; Tian, Wen-Juan; Lu, Hai-Gang; Wu, Yan-Bo; Mu, Yue-Wen; Wei, Guang-Feng; Liu, Zhi-Pan; Li, Jun; Li, Si-Dian; Wang, Lai-Sheng

2014-08-01

After the discovery of fullerene-C60, it took almost two decades for the possibility of boron-based fullerene structures to be considered. So far, there has been no experimental evidence for these nanostructures, in spite of the progress made in theoretical investigations of their structure and bonding. Here we report the observation, by photoelectron spectroscopy, of an all-boron fullerene-like cage cluster at B40(-) with an extremely low electron-binding energy. Theoretical calculations show that this arises from a cage structure with a large energy gap, but that a quasi-planar isomer of B40(-) with two adjacent hexagonal holes is slightly more stable than the fullerene structure. In contrast, for neutral B40 the fullerene-like cage is calculated to be the most stable structure. The surface of the all-boron fullerene, bonded uniformly via delocalized σ and π bonds, is not perfectly smooth and exhibits unusual heptagonal faces, in contrast to C60 fullerene.

Bonding quandary in the [Cu3S2]3+ core: insights from the analysis of domain averaged fermi holes and the local spin.

PubMed

Ponec, Robert; Ramos-Cordoba, Eloy; Salvador, Pedro

2013-03-07

The electronic structure of the trinuclear symmetric complex [(tmedaCu)3S2 ](3+), whose Cu3S2 core represents a model of the active site of metalloenzymes involved in biological processes, has been in recent years the subject of vigorous debate. The complex exists as an open-shell triplet, and discussions concerned the question whether there is a direct S-S bond in the [Cu3S2](3+) core, whose answer is closely related to the problem of the formal oxidation state of Cu atoms. In order to contribute to the elucidation of the serious differences in the conclusions of earlier studies, we report in this study the detailed comprehensive analysis of the electronic structure of the [Cu3S2](3+) core using the methodologies that are specifically designed to address three particular aspects of the bonding in the core of the above complex, namely, the presence and/or absence of direct S-S bond, the existence and the nature of spin-spin interactions among the atoms in the core, and the formal oxidation state of Cu atoms in the core. Using such a combined approach, it was possible to conclude that the picture of bonding consistently indicates the existence of a weak direct two-center-three-electron (2c-3e) S-S bond, but at the same time, the observed lack of any significant local spin in the core of the complex is at odds with the suggested existence of antiferromagnetic coupling among the Cu and S atoms, so that the peculiarities of the bonding in the complex seem to be due to extensive delocalization of the unpaired spin in the [Cu3S2](3+) core. Finally, a scrutiny of the effective atomic hybrids and their occupations points to a predominant formal Cu(II) oxidation state, with a weak contribution of partial Cu(I) character induced mainly by the partial flow of electrons from S to Cu atoms and high delocalization of the unpaired spin in the [Cu3S2](3+) core.

Water-Soluble Fe(II)−H2O Complex with a Weak O−H Bond Transfers a Hydrogen Atom via an Observable Monomeric Fe(III)−OH

PubMed Central

Brines, Lisa M.; Coggins, Michael K.; Poon, Penny Chaau Yan; Toledo, Santiago; Kaminsky, Werner; Kirk, Martin L.

2015-01-01

Understanding the metal ion properties that favor O−H bond formation versus cleavage should facilitate the development of catalysts tailored to promote a specific reaction, e.g., C−H activation or H2O oxidation. The first step in H2O oxidation involves the endothermic cleavage of a strong O−H bond (BDFE = 122.7 kcal/mol), promoted by binding the H2O to a metal ion, and by coupling electron transfer to proton transfer (PCET). This study focuses on details regarding how a metal ion’s electronic structure and ligand environment can tune the energetics of M(HO−H) bond cleavage. The synthesis and characterization of an Fe(II)−H2O complex, 1, that undergoes PCET in H2O to afford a rare example of a monomeric Fe(III)−OH, 7, is described. High-spin 7 is also reproducibly generated via the addition of H2O to {[FeIII(OMe2N4(tren))]2-(µ-O)}2+ (8). The O−H bond BDFE of Fe(II)−H2O (1) (68.6 kcal/mol) is calculated using linear fits to its Pourbaix diagram and shown to be 54.1 kcal/mol less than that of H2O and 10.9 kcal/mol less than that of [Fe(II)(H2O)6]2+. The O−H bond of 1 is noticeably weaker than the majority of reported Mn+(HxO−H) (M = Mn, Fe; n+ = 2+, 3+; x = 0, 1) complexes. Consistent with their relative BDFEs, Fe(II)−H2O (1) is found to donate a H atom to TEMPO•, whereas the majority of previously reported Mn+−O(H) complexes, including [MnIII(SMe2N4(tren))(OH)]+ (2), have been shown to abstract H atoms from TEMPOH. Factors responsible for the weaker O−H bond of 1, such as differences in the electron-donating properties of the ligand, metal ion Lewis acidity, and electronic structure, are discussed. PMID:25611075

A minimalistic approach to static and dynamic electron correlations: Amending generalized valence bond method with extended random phase approximation correlation correction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chatterjee, Koushik; Jawulski, Konrad; Pastorczak, Ewa

A perfect-pairing generalized valence bond (GVB) approximation is known to be one of the simplest approximations, which allows one to capture the essence of static correlation in molecular systems. In spite of its attractive feature of being relatively computationally efficient, this approximation misses a large portion of dynamic correlation and does not offer sufficient accuracy to be generally useful for studying electronic structure of molecules. We propose to correct the GVB model and alleviate some of its deficiencies by amending it with the correlation energy correction derived from the recently formulated extended random phase approximation (ERPA). On the examples ofmore » systems of diverse electronic structures, we show that the resulting ERPA-GVB method greatly improves upon the GVB model. ERPA-GVB recovers most of the electron correlation and it yields energy barrier heights of excellent accuracy. Thanks to a balanced treatment of static and dynamic correlation, ERPA-GVB stays reliable when one moves from systems dominated by dynamic electron correlation to those for which the static correlation comes into play.« less

Multiple hydrogen-bonded complexes based on 2-ureido-4[1H]-pyrimidinone: a theoretical study.

PubMed

Sun, Hao; Lee, Hui Hui; Blakey, Idriss; Dargaville, Bronwin; Chirila, Traian V; Whittaker, Andrew K; Smith, Sean C

2011-09-29

In the present work, the electronic structures and properties of a series of 2-ureido-4[1H]-pyrimidinone(UPy)-based monomers and dimers in various environments (vacuum, chloroform, and water) are studied by density functional theoretical methods. Most dimers prefer to form a DDAA-AADD (D, H-bond donor; A, H-bond acceptor) array in both vacuum and solvents. Topological analysis proved that intramolecular and intermolecular hydrogen bonds coexist in the dimers. Frequency and NBO calculations show that all the hydrogen bonds exhibit an obvious red shift in their stretching vibrational frequencies. Larger substituents at position 6 of the pyrimidinone ring with stronger electron-donating ability favor the total binding energy and free energy of dimerization. Calculations on the solvent effect show that dimerization is discouraged by the stronger polarity of the solvent. Further computations show that Dimer-1 may be formed in chloroform, but water molecules may interact with the donor or acceptor sites and hence disrupt the hydrogen bonds of Dimer-1. © 2011 American Chemical Society

H2MBH2 and M(μ-H)2BH2 Molecules Isolated in Solid Argon: Interelement M-B and M-H-B Bonds (M = Ge, Sn).

PubMed

Zhao, Jie; Beckers, Helmut; Huang, Tengfei; Wang, Xuefeng; Riedel, Sebastian

2018-02-19

Laser-ablated boron atoms react with GeH 4 molecules to form novel germylidene borane H 2 GeBH 2 , which undergoes a photochemical rearrangement to the germanium tetrahydroborate Ge(μ-H) 2 BH 2 upon irradiation with light of λ = 405 nm. For comparison, the boron atom reactions with SnH 4 only gave the tin tetrahydroborate Sn(μ-H) 2 BH 2 . Infrared matrix-isolation spectroscopy with deuterium substitution and the state-of-the-art quantum-chemical calculations are used to identify these species in solid argon. A planar structure of H 2 GeBH 2 with an electron-deficient B-Ge bond with a partial multiple bond character (bond order = 1.5) is predicted by quantum-chemical calculations. In the case of M(μ-H) 2 BH 2 (M = Ge, Sn) two 3c-2e B-H-M hydrogen bridged bonds are formed by donation of electrons from the B-H σ-bonds into empty p-orbitals of M.

Interfacial structure, bonding and composition of InAs and GaSb thin films determined using coherent Bragg rod analysis.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cionca, C.; Walko, D. A.; Yacoby, Y.

2007-01-01

We have used Bragg rod x-ray diffraction combined with a direct method of phase retrieval to extract atomic resolution electron-density maps of a complementary series of heteroepitaxial III-V semiconductor samples. From the three-dimensional electron-density maps we derive the monolayer spacings, the chemical compositions, and the characteristics of the bonding for all atomic planes in the film and across the film-substrate interface. InAs films grown on GaSb(001) under two different As conditions (using dimer or tetramer forms) both showed conformal roughness and mixed GaAs/InSb interfacial bonding character. The As tetramer conditions favored InSb bonding at the interface while, in the casemore » of the dimer, the percentages corresponding to GaAs and InSb bonding were equal within the experimental error. The GaSb film grown on InAs(001) displayed significant In and As interdiffusion and had a relatively large fraction of GaAs-like bonds at the interface.« less

Crystallographic perturbations to valence charge density and hydrogen-surface interactions

NASA Astrophysics Data System (ADS)

Ciston, James W.

The subject of surfaces has been the epicenter of numerous studies in recent years, particularly with respect to applications in catalysis, thin films, and self-assembly of nanostructures where the surface-to-volume ratio is large. Understanding how the atomic structure of materials differs at surfaces where the atoms are far less constrained can yield fundamental insight into these interesting nanoscale phenomena. Quantum surface crystallography takes this one step further in an attempt to experimentally measure the structure of the electrons themselves, which is of greater importance than atomic positions in determining material properties. We report a procedure for obtaining a much better initial parameterization of the charge density than what is possible from a neutral atom model. This procedure involves the parameterization of a bulk charge density model in terms of simple variables such as bond lengths, which can then be transferred to the problem of interest, for instance a surface. Parameterization is accomplished through the fitting of Density Functional Theory calculations of a variety of crystal distortions to a bond-centered pseudoatom (BCPA) model. This parameterized model can then be applied to surfaces or for other problems where an initial higher-order model is needed without the addition of any extra fitted parameters. Through the use of the BCPA model, we report a three-dimensional charge density refinement from x-ray diffraction intensities of the Si (001) 2x1H surface. By properly accounting for the covalent bonding effects in the silicon structure, we were able to stably refine the positions of hydrogen atoms at this surface in three dimensions, which had never before been accomplished for any surface. In addition, we found experimentally an increased, slightly localized bond density of approximately 0.31 electrons between each Si atom pair at the surface. Both the atomic positions and the charge density were found to be in remarkably good agreement with density functional theory (DFT) calculations. The BCPA model was also applied to an experimental refinement of the local charge density at the Si (111) 7x7 surface utilizing a combination of x-ray and high energy electron diffraction. By perturbing about the bond-centered pseudoatom model, we found experimentally that the adatoms were in an anti-bonding state with the atoms directly below. We were also able to experimentally refine a charge transfer of 0.26+/-0.04 e- from each adatom site to the underlying layers. This was the first statistically significant refinement of site-specific bonding information at any surface utilizing x-ray diffraction data. Precession electron diffraction (PED) is a technique which is gaining increasing interest due to its ease of use and reduction of the dynamical scattering problem in electron diffraction. To further investigate the usefulness of this technique, we performed a systematic study of the effect of precession angle on the mineral andalusite where the semiangle was varied from 6.5 to 32 mrad in five discrete steps. We have shown that the intensities of kinematically forbidden reflections decayed exponentially as the precession semiangle (ϕ) was increased. Additionally, we have determined that charge density effects were best observed at moderately low angles (6.5-13 mrad) even though PED patterns became more kinematical in nature as the precession angle was increased further. We have also shown that the amount of interpretable information provided by direct methods phase inversion of the diffraction data increases monotonically but non-systematically as ϕ increases. We report an experimental and theoretical analysis of the ✓3x✓3-R30° and 2x2 reconstructions on the MgO (111) surface combining transmission electron microscopy, x-ray photoelectron spectroscopy, and reasonably accurate density functional calculations using the meta-GGA functional TPSS. We have not only conclusively solved the atomic structures of these reconstructions, but have developed a kinetic model for an evolutionary pathway between structures driven entirely by exchange of water molecules between the surface and the environment that does not require the cations to move when the structure transforms. This is the first time an experimentally and theoretically supported kinetic model has described not only all of the structures in a series on a single oxide surface, but also describes why none of the structures pass through the thermodynamically most stable configuration. Lastly, we have investigated the observability of valence bonding effects in aberration-corrected high resolution electron microscopy (HREM) images along the [010] projection of the mineral Forsterite (Mg2SiO 4). Direct observability of bonding effects would be both faster and less ambiguous than the refinement of similar features against diffraction data. Through analysis of simulated high resolution electron microscopy images, we have determined that bonding effects should be observable at levels approaching 20% of the total contrast. Initial experimental results for this material system have also been presented.

Proper Resonance Depiction of Acylium Cation: A High-Level and Student Computational Investigation

ERIC Educational Resources Information Center

Esselman, Brian J.; Hill, Nicholas J.

2015-01-01

The electronic and molecular structure of the acylium cation ([CH[subscript 3]CO][superscript +], 1) receives varied treatment in undergraduate textbooks and online resources. The overall structure of 1 is typically represented as an equal combination of resonance structures containing C-O triple and double bonds, the latter structure occasionally…

Insights into the Electronic Structure of Ozone and Sulfur Dioxide from Generalized Valence Bond Theory: Addition of Hydrogen Atoms.

PubMed

Lindquist, Beth A; Takeshita, Tyler Y; Dunning, Thom H

2016-05-05

Ozone (O3) and sulfur dioxide (SO2) are valence isoelectronic species, yet their properties and reactivities differ dramatically. In particular, O3 is highly reactive, whereas SO2 is chemically relatively stable. In this paper, we investigate serial addition of hydrogen atoms to both the terminal atoms of O3 and SO2 and to the central atom of these species. It is well-known that the terminal atoms of O3 are much more amenable to bond formation than those of SO2. We show that the differences in the electronic structure of the π systems in the parent triatomic species account for the differences in the addition of hydrogen atoms to the terminal atoms of O3 and SO2. Further, we find that the π system in SO2, which is a recoupled pair bond dyad, facilitates the addition of hydrogen atoms to the sulfur atom, resulting in stable HSO2 and H2SO2 species.

Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds: study in explicit water.

PubMed

Duan, Li L; Gao, Ya; Mei, Ye; Zhang, Qing G; Tang, Bo; Zhang, John Z H

2012-03-15

Multiple single-trajectory molecular dynamics (MD) simulation at room temperature (300 K) in explicit water was carried out to study the folding dynamics of an α-helix (PDB 2I9M ) using a polarized charge scheme that includes electronic polarization of backbone hydrogen bonds. Starting from an extended conformation, the 17-residue peptide was successfully folded into the native structure (α-helix) between 80 and 130 ns with a root-mean-square deviation of ~1.0 Å. Analysis of the time-dependent trajectories revealed that helix formation of the peptide started at the terminals and progressed toward the center of the peptide. For comparison, MD trajectories generated under various versions of standard AMBER force fields failed to show any significant or stable helix formation in our simulation. Our result shows clear evidence that the electronic polarization of backbone hydrogen bonds energetically stabilizes the helix formation and is critical to the stable folding of the short helix structure. © 2012 American Chemical Society

A Systematic Theoretical Study of UC6: Structure, Bonding Nature, and Spectroscopy.

PubMed

Du, Jiguang; Jiang, Gang

2017-11-20

The study of uranium carbides has received renewed attention in recent years due to the potential use of these compounds as fuels in new generations of nuclear reactors. The isomers of the UC 6 cluster were determined by DFT and ab initio methods. The structures obtained using SC-RECP for U were generally consistent with those obtained using an all-electron basis set (ZORA-SARC). The CCSD(T) calculations indicated that two isomers had similar energies and may coexist in laser evaporation experiments. The nature of the U-C bonds in the different isomers was examined via a topological analysis of the electron density, and the results indicated that the U-C bonds are predominantly closed-shell (ionic) interactions with a certain degree of covalent character in all cases, particularly in the linear species. The IR and UV-vis spectra of the isomers were theoretically simulated to provide information that can be used to identify the isomers of UC 6 in future experiments.

Atomic resolution chemical bond analysis of oxygen in La2CuO4

NASA Astrophysics Data System (ADS)

Haruta, M.; Nagai, T.; Lugg, N. R.; Neish, M. J.; Nagao, M.; Kurashima, K.; Allen, L. J.; Mizoguchi, T.; Kimoto, K.

2013-08-01

The distorted CuO6 octahedron in La2CuO4 was studied using aberration-corrected scanning transmission electron microscopy at atomic resolution. The near-edge structure in the oxygen K-edge electron energy-loss spectrum was recorded as a function of the position of the electron probe. After background subtraction, the measured spectrum image was processed using a recently developed inversion process to remove the mixing of signals on the atomic columns due to elastic and thermal scattering. The spectra were then compared with first-principles band structure calculations based on the local-density approximation plus on-site Coulomb repulsion (LDA + U) approach. In this article, we describe in detail not only anisotropic chemical bonding of the oxygen 2p state with the Cu 3d state but also with the Cu 4p and La 5d/4f states. Furthermore, it was found that buckling of the CuO2 plane was also detectable at the atomic resolution oxygen K-edge. Lastly, it was found that the effects of core-hole in the O K-edge were strongly dependent on the nature of the local chemical bonding, in particular, whether it is ionic or covalent.

Synthesis of quenchable amorphous diamond

DOE PAGES

Zeng, Zhidan; Yang, Liuxiang; Zeng, Qiaoshi; ...

2017-08-22

Diamond owes its unique mechanical, thermal, optical, electrical, chemical, and biocompatible materials properties to its complete sp 3-carbon network bonding. Crystallinity is another major controlling factor for materials properties. Although other Group-14 elements silicon and germanium have complementary crystalline and amorphous forms consisting of purely sp 3 bonds, purely sp 3-bonded tetrahedral amorphous carbon has not yet been obtained. In this letter, we combine high pressure and in situ laser heating techniques to convert glassy carbon into “quenchable amorphous diamond”, and recover it to ambient conditions. Our X-ray diffraction, high-resolution transmission electron microscopy and electron energy-loss spectroscopy experiments on themore » recovered sample and computer simulations confirm its tetrahedral amorphous structure and complete sp 3 bonding. This transparent quenchable amorphous diamond has, to our knowledge, the highest density among amorphous carbon materials, and shows incompressibility comparable to crystalline diamond.« less

Synthesis of quenchable amorphous diamond

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeng, Zhidan; Yang, Liuxiang; Zeng, Qiaoshi

Diamond owes its unique mechanical, thermal, optical, electrical, chemical, and biocompatible materials properties to its complete sp 3-carbon network bonding. Crystallinity is another major controlling factor for materials properties. Although other Group-14 elements silicon and germanium have complementary crystalline and amorphous forms consisting of purely sp 3 bonds, purely sp 3-bonded tetrahedral amorphous carbon has not yet been obtained. In this letter, we combine high pressure and in situ laser heating techniques to convert glassy carbon into “quenchable amorphous diamond”, and recover it to ambient conditions. Our X-ray diffraction, high-resolution transmission electron microscopy and electron energy-loss spectroscopy experiments on themore » recovered sample and computer simulations confirm its tetrahedral amorphous structure and complete sp 3 bonding. This transparent quenchable amorphous diamond has, to our knowledge, the highest density among amorphous carbon materials, and shows incompressibility comparable to crystalline diamond.« less

Joining of Silicon Carbide Through the Diffusion Bonding Approach

NASA Technical Reports Server (NTRS)

Halbig, Michael .; Singh, Mrityunjay

2009-01-01

In order for ceramics to be fully utilized as components for high-temperature and structural applications, joining and integration methods are needed. Such methods will allow for the fabrication the complex shapes and also allow for insertion of the ceramic component into a system that may have different adjacent materials. Monolithic silicon carbide (SiC) is a ceramic material of focus due to its high temperature strength and stability. Titanium foils were used as an interlayer to form diffusion bonds between chemical vapor deposited (CVD) SiC ceramics with the aid of hot pressing. The influence of such variables as interlayer thickness and processing time were investigated to see which conditions contributed to bonds that were well adhered and crack free. Optical microscopy, scanning electron microscopy, and electron microprobe analysis were used to characterize the bonds and to identify the reaction formed phases.

Bond Ellipticity Alternation: An Accurate Descriptor of the Nonlinear Optical Properties of π-Conjugated Chromophores.

PubMed

Lopes, Thiago O; Machado, Daniel F Scalabrini; Risko, Chad; Brédas, Jean-Luc; de Oliveira, Heibbe C B

2018-03-15

Well-defined structure-property relationships offer a conceptual basis to afford a priori design principles to develop novel π-conjugated molecular and polymer materials for nonlinear optical (NLO) applications. Here, we introduce the bond ellipticity alternation (BEA) as a robust parameter to assess the NLO characteristics of organic chromophores and illustrate its effectiveness in the case of streptocyanines. BEA is based on the symmetry of the electron density, a physical observable that can be determined from experimental X-ray electron densities or from quantum-chemical calculations. Through comparisons to the well-established bond-length alternation and π-bond order alternation parameters, we demonstrate the generality of BEA to foreshadow NLO characteristics and underline that, in the case of large electric fields, BEA is a more reliable descriptor. Hence, this study introduces BEA as a prominent descriptor of organic chromophores of interest for NLO applications.

Density functional theory study of the structural and bonding mechanism of molecular oxygen (O2) with C3Si

NASA Astrophysics Data System (ADS)

Parida, Saroj K.; Behera, C.; Sahu, Sridhar

2018-07-01

The investigations of pure and heteroatom doped carbon clusters have created great interest because of their enormous prospective applications in various research zones, for example, optoelectronics, semiconductors, material science, energy storage devices, astro-science and so on. In this article, the interaction of molecular oxygen (O2) with C3Si has explored within a density functional theory (DFT). Different possible types of structure for C3SiO2 have collected. Among five different kinds of structure, the structure-1a, 1A1 is more energetically stable. The nature of the bonding of O2 and C3Si, in C3SiO2 has been studied by using Bader's topological analysis of the electron charge density distribution ρ(r) , Laplacian ∇2 ρ(r) and total energy density H(r) at the bond critical points (BCPs) of the structures within the framework of the atoms in molecules theory (AIM). The bonding mechanism of O2 and C3Si in C3SiO2 prompts to the fundamental understanding of the interaction of C3Si with oxygen molecule. It is interesting to note that, two types of bonding mechanism are established in same C3SiO2 system such as (i) shared-kind interactions (ii) closed-shell interactions. From various kinds of structure, Csbnd C bonds in all structures are shown as shared-kind interactions whereas Csbnd Si, Osbnd O bonds are classified as closed-shell type interactions with a certain degree of covalent character.

Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the "On-the-Fly" Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD).

PubMed

Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S

2014-06-10

We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good agreement with experiments. Spectroscopic features are computed using a unified velocity/flux autocorrelation function and include vibrational fundamentals and combination bands. These agree well with experiments and other theories.

SU-C-204-03: DFT Calculations of the Stability of DOTA-Based-Radiopharmaceuticals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khabibullin, A.R.; Woods, L.M.; Karolak, A.

2016-06-15

Purpose: Application of the density function theory (DFT) to investigate the structural stability of complexes applied in cancer therapy consisting of the 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelated to Ac225, Fr221, At217, Bi213, and Gd68 radio-nuclei. Methods: The possibility to deliver a toxic payload directly to tumor cells is a highly desirable aim in targeted alpha particle therapy. The estimation of bond stability between radioactive atoms and the DOTA chelating agent is the key element in understanding the foundations of this delivery process. Thus, we adapted the Vienna Ab-initio Simulation Package (VASP) with the projector-augmented wave method and a plane-wave basis setmore » in order to study the stability and electronic properties of DOTA ligand chelated to radioactive isotopes. In order to count for the relativistic effect of radioactive isotopes we included Spin-Orbit Coupling (SOC) in the DFT calculations. Five DOTA complex structures were represented as unit cells, each containing 58 atoms. The energy optimization was performed for all structures prior to calculations of electronic properties. Binding energies, electron localization functions as well as bond lengths between atoms were estimated. Results: Calculated binding energies for DOTA-radioactive atom systems were −17.792, −5.784, −8.872, −13.305, −18.467 eV for Ac, Fr, At, Bi and Gd complexes respectively. The displacements of isotopes in DOTA cages were estimated from the variations in bond lengths, which were within 2.32–3.75 angstroms. The detailed representation of chemical bonding in all complexes was obtained with the Electron Localization Function (ELF). Conclusion: DOTA-Gd, DOTA-Ac and DOTA-Bi were the most stable structures in the group. Inclusion of SOC had a significant role in the improvement of DFT calculation accuracy for heavy radioactive atoms. Our approach is found to be proper for the investigation of structures with DOTA-based-radiopharmaceuticals and will enhance our understanding of processes occurring at subatomic levels.« less

Low energy electron induced cytosine base release in 2′-deoxycytidine-3′-monophosphate via glycosidic bond cleavage: A time-dependent wavepacket study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhaskaran, Renjith; Sarma, Manabendra, E-mail: msarma@iitg.ernet.in

2014-09-14

Low energy electron (LEE) induced cytosine base release in a selected pyrimidine nucleotide, viz., 2′-deoxycytidine-3′-monophosphate is investigated using ab initio electronic structure methods and time dependent quantum mechanical calculations. It has been noted that the cytosine base scission is comparatively difficult process than the 3′ C–O bond cleavage from the lowest π{sup *} shape resonance in energy region <1 eV. This is mainly due to the high activation energy barrier associated with the electron transfer from the π{sup *} orbital of the base to the σ{sup *} orbital of the glycosidic N–C bond. In addition, the metastable state formed aftermore » impinging LEE (0–1 eV) has very short lifetime (10 fs) which may decay in either of the two competing auto-detachment or dissociation process simultaneously. On the other hand, the selected N–C mode may cleave to form the cytosine base anion at higher energy regions (>2 eV) via tunneling of the glycosidic bond. Resonance states generated within this energy regime will exist for a duration of ∼35–55 fs. Comparison of salient features of the two dissociation events, i.e., 3′ C–O single strand break and glycosidic N–C bond cleavage in 3′-dCMPH molecule are also provided.« less

Natural bond orbital analysis in the ONETEP code: applications to large protein systems.

PubMed

Lee, Louis P; Cole, Daniel J; Payne, Mike C; Skylaris, Chris-Kriton

2013-03-05

First principles electronic structure calculations are typically performed in terms of molecular orbitals (or bands), providing a straightforward theoretical avenue for approximations of increasing sophistication, but do not usually provide any qualitative chemical information about the system. We can derive such information via post-processing using natural bond orbital (NBO) analysis, which produces a chemical picture of bonding in terms of localized Lewis-type bond and lone pair orbitals that we can use to understand molecular structure and interactions. We present NBO analysis of large-scale calculations with the ONETEP linear-scaling density functional theory package, which we have interfaced with the NBO 5 analysis program. In ONETEP calculations involving thousands of atoms, one is typically interested in particular regions of a nanosystem whilst accounting for long-range electronic effects from the entire system. We show that by transforming the Non-orthogonal Generalized Wannier Functions of ONETEP to natural atomic orbitals, NBO analysis can be performed within a localized region in such a way that ensures the results are identical to an analysis on the full system. We demonstrate the capabilities of this approach by performing illustrative studies of large proteins--namely, investigating changes in charge transfer between the heme group of myoglobin and its ligands with increasing system size and between a protein and its explicit solvent, estimating the contribution of electronic delocalization to the stabilization of hydrogen bonds in the binding pocket of a drug-receptor complex, and observing, in situ, the n → π* hyperconjugative interactions between carbonyl groups that stabilize protein backbones. Copyright © 2012 Wiley Periodicals, Inc.

Density functional study of structural and electronic properties of bimetallic silver-gold clusters: Comparison with pure gold and silver clusters

NASA Astrophysics Data System (ADS)

Bonacic-Koutecky, Vlasta; Burda, Jaroslav; Mitric, Roland; Ge, Maofa; Zampella, Giuseppe; Fantucci, Piercarlo

2002-08-01

Bimetallic silver-gold clusters offer an excellent opportunity to study changes in metallic versus "ionic" properties involving charge transfer as a function of the size and the composition, particularly when compared to pure silver and gold clusters. We have determined structures, ionization potentials, and vertical detachment energies for neutral and charged bimetallic AgmAun 3[less-than-or-equal](m+n)[less-than-or-equal]5 clusters. Calculated VDE values compare well with available experimental data. In the stable structures of these clusters Au atoms assume positions which favor the charge transfer from Ag atoms. Heteronuclear bonding is usually preferred to homonuclear bonding in clusters with equal numbers of hetero atoms. In fact, stable structures of neutral Ag2Au2, Ag3Au3, and Ag4Au4 clusters are characterized by the maximum number of hetero bonds and peripheral positions of Au atoms. Bimetallic tetramer as well as hexamer are planar and have common structural properties with corresponding one-component systems, while Ag4Au4 and Ag8 have 3D forms in contrast to Au8 which assumes planar structure. At the density functional level of theory we have shown that this is due to participation of d electrons in bonding of pure Aun clusters while s electrons dominate bonding in pure Agm as well as in bimetallic clusters. In fact, Aun clusters remain planar for larger sizes than Agm and AgnAun clusters. Segregation between two components in bimetallic systems is not favorable, as shown in the example of Ag5Au5 cluster. We have found that the structures of bimetallic clusters with 20 atoms Ag10Au10 and Ag12Au8 are characterized by negatively charged Au subunits embedded in Ag environment. In the latter case, the shape of Au8 is related to a pentagonal bipyramid capped by one atom and contains three exposed negatively charged Au atoms. They might be suitable for activating reactions relevant to catalysis. According to our findings the charge transfer in bimetallic clusters is responsible for formation of negatively charged gold subunits which are expected to be reactive, a situation similar to that of gold clusters supported on metal oxides.

Welding, Bonding and Fastening, 1984

NASA Technical Reports Server (NTRS)

Buckley, J. D. (Editor); Stein, B. A. (Editor)

1985-01-01

A compilation of papers presented in a joint NASA, American Society for Metals, The George Washington University, American Welding Soceity, and Society of Manufacturing Engineers conference on Welding, Bonding, and Fastening at Langley Research Center, Hampton, VA, on October 23 to 25, 1984 is given. Papers were presented on technology developed in current research programs relevant to welding, bonding, and fastening of structural materials required in fabricating structures and mechanical systems used in the aerospace, hydrospace, and automotive industries. Topics covered in the conference included equipment, hardware and materials used when welding, brazing, and soldering, mechanical fastening, explosive welding, use of unique selected joining techniques, adhesives bonding, and nondestructive evaluation. A concept of the factory of the future was presented, followed by advanced welding techniques, automated equipment for welding, welding in a cryogenic atmosphere, blind fastening, stress corrosion resistant fasteners, fastening equipment, explosive welding of different configurations and materials, solid-state bonding, electron beam welding, new adhesives, effects of cryogenics on adhesives, and new techniques and equipment for adhesive bonding.

Multi-scale predictive modeling of nano-material and realistic electron devices

NASA Astrophysics Data System (ADS)

Palaria, Amritanshu

Among the challenges faced in further miniaturization of electronic devices, heavy influence of the detailed atomic configuration of the material(s) involved, which often differs significantly from that of the bulk material(s), is prominent. Device design has therefore become highly interrelated with material engineering at the atomic level. This thesis aims at outlining, with examples, a multi-scale simulation procedure that allows one to integrate material and device aspects of nano-electronic design to predict behavior of novel devices with novel material. This is followed in four parts: (1) An approach that combines a higher time scale reactive force field analysis with density functional theory to predict structure of new material is demonstrated for the first time for nanowires. Novel stable structures for very small diameter silicon nanowires are predicted. (2) Density functional theory is used to show that the new nanowire structures derived in 1 above have properties different from diamond core wires even though the surface bonds in some may be similar to the surface of bulk silicon. (3) Electronic structure of relatively large-scale germanium sections of realistically strained Si/strained Ge/ strained Si nanowire heterostructures is computed using empirical tight binding and it is shown that the average non-homogeneous strain in these structures drives their interesting non-conventional electronic characteristics such as hole effective masses which decrease as the wire cross-section is reduced. (4) It is shown that tight binding, though empirical in nature, is not necessarily limited to the material and atomic structure for which the parameters have been empirically derived, but that simple changes may adapt the derived parameters to new bond environments. Si (100) surface electronic structure is obtained from bulk Si parameters.

The Crystal Structures of Potentially Tautomeric Compounds

NASA Astrophysics Data System (ADS)

Furmanova, Nina G.

1981-08-01

Data on the structures of potentially proto-, metallo-, and carbono-tropic compounds, obtained mainly by X-ray diffraction, are surveyed. The results of neutron and electron diffraction studies have also been partly used. It is shown that a characteristic feature of all the systems considered is the formation of hydrogen or secondary bonds ensuring the contribution of both possible tautomeric forms to the structure. Systematic consideration of the experimental data leads to the conclusion that there is a close relation between the crystal structure and the dynamic behaviour of the molecules in solution and that secondary and hydrogen bonds play a significant role in the tautomeric transition. The bibliography includes 152 references.

Nickel superoxide dismutase: structural and functional roles of His1 and its H-bonding network

DOE PAGES

Maroney, Michael J.; Cabelli, Diane E.; Ryan, Kelly C.; ...

2015-01-21

Crystal structures of nickel-dependent superoxide dismutases (NiSODs) reveal the presence of a H-bonding network formed between the NH group of the apical imidazole ligand from His1 and the Glu17 carboxylate from a neighboring subunit in the hexameric enzyme. This interaction is supported by another intrasubunit H-bond between Glu17 and Arg47. In this study, four mutant NiSOD proteins were produced to experimentally evaluate the roles of this H-bonding network and compare the results with prior predictions from density functional theory calculations. The X-ray crystal structure of H1A-NiSOD, which lacks the apical ligand entirely, reveals that in the absence of the Glu17-His1more » H-bond, the active site is disordered. Characterization of this variant using X-ray absorption spectroscopy (XAS) shows that Ni(II) is bound in the expected N₂S₂ planar coordination site. Despite these structural perturbations, the H1A-NiSOD variant retains 4% of wild-type (WT) NiSOD activity. Three other mutations were designed to preserve the apical imidazole ligand but perturb the H-bonding network: R47A-NiSOD, which lacks the intramolecular H-bonding interaction; E17R/R47A-NiSOD, which retains the intramolecular H-bond but lacks the intermolecular Glu17-His1 H-bond; and E17A/R47ANiSOD, which lacks both H-bonding interactions. These variants were characterized by a combination of techniques, including XAS to probe the nickel site structure, kinetic studies employing pulse-radiolytic production of superoxide, and electron paramagnetic resonance to assess the Ni redox activity. The results indicate that in addition to the roles in redox tuning suggested on the basis of previous computational studies, the Glu17-His1 H-bond plays an important structural role in the proper folding of the “Ni-hook” motif that is a critical feature of the active site.« less

Planar CoB18- Cluster: a New Motif for - and Metallo-Borophenes

NASA Astrophysics Data System (ADS)

Chen, Teng-Teng; Jian, Tian; Lopez, Gary; Li, Wan-Lu; Chen, Xin; Li, Jun; Wang, Lai-Sheng

2016-06-01

Combined Photoelectron Spectroscopy (PES) and theoretical calculations have found that anion boron clusters (Bn-) are planar and quasi-planar up to B25-. Recent works show that anion pure boron clusters continued to be planar at B27-,B30-,B35- and B36-. B35- and B36- provide the first experimental evidence for the viability of the two-dimensional (2D) boron sheets (Borophene). The 2D to three-dimensional (3D) transitions are shown to happen at B40-,B39- and B28-, which possess cage-like structures. These fullerene-like boron cage clusters are named as Borospherene. Recently, borophenes or similar structures are claimed to be synthesized by several groups. Following an electronic design principle, a series of transition-metal-doped boron clusters (M©Bn-, n=8-10) are found to possess the monocyclic wheel structures. Meanwhile, CoB12- and RhB12- are revealed to adopt half-sandwich-type structures with the quasi-planar B12 moiety similar to the B12- cluster. Very lately, we show that the CoB16- cluster possesses a highly symmetric Cobalt-centered drum-like structure, with a new record of coordination number at 16. Here we report the CoB18- cluster to possess a unique planar structure, in which the Co atom is doped into the network of a planar boron cluster. PES reveals that the CoB18- cluster is a highly stable electronic system with the first adiabatic detachment energy (ADE) at 4.0 eV. Global minimum searches along with high-level quantum calculations show the global minimum for CoB18- is perfectly planar and closed shell (1A1) with C2v symmetry. The Co atom is bonded with 7 boron atoms in the closest coordination shell and the other 11 boron atoms in the outer coordination shell. The calculated vertical detachment energy (VDE) values match quite well with our experimental results. Chemical bonding analysis by the Adaptive Natural Density Partitioning (AdNDP) method shows the CoB18- cluster is π-aromatic with four 4-centered-2-electron (4c-2e) π bonds and one 19-centered-2-electron (19c-2e) π bond, 10 π electrons in total. This perfectly planar structure reveals the viability of creating a new class of hetero-borophenes and metallo-borophenes by doping metal atoms into the plane of monolayer boron atoms. This gives a new approach to design perspective hetero-borophenes and metallo-borophenes materials with tunable chemical, magnetic and optical properties.

Writing Electron Dot Structures: Abstract of Issue 9905M

NASA Astrophysics Data System (ADS)

Magnell, Kenneth R.

1999-10-01

Writing Electron Dot Structures is a computer program for Mac OS that provides drill with feedback for students learning to write electron dot structures. While designed for students in the first year of college general chemistry it may also be used by high school chemistry students. A systematic method similar to that found in many general chemistry texts is employed:

1. determine the number of valence shell electrons,
2. select the central atom,
3. construct a skeleton,
4. add electrons to complete octets,
5. examine the structure for resonance forms.

A study of N-methylacetamide in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Yang, Zhong-Zhi; Qian, Ping

2006-08-14

N-methylacetamide (NMA) is a very interesting compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of the peptides in aqueous solutions. Here we present NMA-water potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) that is to take ABEEM charges of all atoms, bonds, and lone-pair electrons of NMA and water molecules into the electrostatic interaction term in molecular mechanics. The model has the following characters: (1)it allows the charges in system to fluctuate responding to the ambient environment; (2) for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters k(lpO=, H) and k(lpO(-), HN(-)), respectively. The newly constructed potential model based on ABEEM/MM is first applied to amide-water clusters and reproduces gas-phase state properties of NMA(H(2)O)(n) (n=1-3) including optimal structures, dipole moments, ABEEM charge distributions, energy difference of the isolated trans- and cis-NMA, interaction energies, hydrogen bonding cooperative effects, and so on, whose results show the good agreement with those measured by available experiments and calculated by ab initio methods. In order to further test the reasonableness of this model and the correctness and transferability of the parameters, many static properties of the larger NMA-water complexes NMA(H(2)O)(n) (n=4-6) are also studied including optimal structures and interaction energies. The results also show fair consistency with those of our quantum chemistry calculations.

Ultrafast laser-induced modifications of energy bands of non-metal crystals

NASA Astrophysics Data System (ADS)

Gruzdev, Vitaly

2009-10-01

Ultrafast laser-induced variations of electron energy bands of transparent solids significantly influence ionization and conduction-band electron absorption driving the initial stage of laser-induced damage (LID). The mechanisms of the variations are attributed to changing electron functions from bonding to anti-bonding configuration via laser-induced ionization; laser-driven electron oscillations in quasi-momentum space; and direct distortion of the inter-atomic potential by electric field of laser radiation. The ionization results in the band-structure modification via accumulation of broken chemical bonds between atoms and provides significant contribution to the overall modification only when enough excited electrons are accumulated in the conduction band. The oscillations are associated with modification of electron energy by pondermotive potential of the oscillations. The direct action of radiation's electric field leads to specific high-frequency Franz-Keldysh effect (FKE) spreading the allowed electron states into the bands of forbidden energy. Those processes determine the effective band gap that is a laser-driven energy gap between the modified electron energy bands. Among those mechanisms, the latter two provide reversible band-structure modification that takes place from the beginning of the ionization and are, therefore, of special interest due to their strong influence on the initial stage of the ionization. The pondermotive potential results either in monotonous increase or oscillatory variations of the effective band gap that has been taken into account in some ionization models. The classical FKE provides decrease of the band gap. We analyzing the competition between those two opposite trends of the effective-band-gap variations and discuss applications of those effects for considerations of the laser-induced damage and its threshold in transparent solids.

Association of 2-acylaminopyridines and benzoic acids. Steric and electronic substituent effect studied by XRD, solution and solid-state NMR and calculations

NASA Astrophysics Data System (ADS)

Ośmiałowski, Borys; Kolehmainen, Erkki; Ejsmont, Krzysztof; Ikonen, Satu; Valkonen, Arto; Rissanen, Kari; Nonappa

2013-12-01

Eight single crystal X-ray structures, solid-state NMR spectroscopic, and theoretical studies utilizing QTAIM methodology were used to characterize the 2-acyl (alkyl in acyl = methyl, ethyl, t-butyl, and 1-adamantyl) amino-6-R-pyridine/4-R‧-benzoic acid (R,R‧ = H or Me) cocrystals. As expected among alkyl groups 1-adamantyl due to its bulkiness has the most significant effect on the relative positions of molecules in cocrystals. In addition, the subtle electronic and steric effects by the methyl substituents were observed. The theoretical calculations with full geometry optimizations are in agreement with the experimental findings (geometry, energy of hydrogen bonds). Based on the crystal structures and calculations it is concluded that p-methyl substituent in benzoic acid increase the hydrogen bond accepting ability of the CO oxygen and decreases the hydrogen bond donating ability of OH proton. The 15N solid-state (CP MAS) NMR chemical shifts prove that molecules in cocrystal are held together by hydrogen bonding. The biggest variation in the 15N chemical shift of acylamino nitrogen can be related with the size of the alkyl group in acyl moiety.

D3h [A-CE3-A]- (E = Al and Ga, A = Si, Ge, Sn, and Pb): A new class of hexatomic mono-anionic species with trigonal bipyramidal carbon

NASA Astrophysics Data System (ADS)

Wu, Yan-Bo; Li, Yan-Qin; Bai, Hui; Lu, Hai-Gang; Li, Si-Dian; Zhai, Hua-Jin; Wang, Zhi-Xiang

2014-03-01

The non-classical trigonal bipyramidal carbon (TBPC) arrangement generally exists as transition states (TSs) in nucleophilic bimolecular substitution (SN2) reactions. Nevertheless, chemists have been curious about whether such a carbon bonding could be stable in equilibrium structures for decades. As the TBPC arrangement was normally realized as cationic species theoretically and experimentally, only one anionic example ([At-C(CN)3-At]-) was computationally devised. Herein, we report the design of a new class of anionic TBPC species by using the strategy similar to that for stabilizing the non-classical planar hypercoordinate carbon. When electron deficient Al and Ga were used as the equatorial ligands, eight D3h [A-CE3-A]- (E = Al and Ga, A = Si, Ge, Sn, and Pb) TBPC structures were found to be the energy minima rather than TSs at both the B3LYP and MP2 levels. Remarkably, the energetic results at the CCSD(T) optimization level further identify [Ge-CAl3-Ge]- and [Sn-CGa3-Sn]- even to be the global minima and [Si-CAl3-Si]- and [Ge-CGa3-Ge]- to be the local minima, only slightly higher than their global minima. The electronic structure analyses reveal that the substantial ionic C-E bonding, the peripheral E-A covalent bonding, and the axial mc-2e (multi center-two electrons) bonding play roles in stabilizing these TBPC structures. The structural simplicity and the high thermodynamic stability suggest that some of these species may be generated and captured in the gas phase. Furthermore, as mono-anionic species, their first vertical detachment energies are differentiable from those of their nearest isomers, which would facilitate their characterization via experiments such as the negative ion photoelectron spectroscopy.

A liquid-liquid transition can exist in monatomic transition metals with a positive melting slope

PubMed Central

Lee, Byeongchan; Lee, Geun Woo

2016-01-01

Liquid-liquid transitions under high pressure are found in many elemental materials, but the transitions are known to be associated with either sp-valent materials or f-valent rare-earth elements, in which the maximum or a negative slope in the melting line is readily suggestive of the transition. Here we find a liquid-liquid transition with a positive melting slope in transition metal Ti from structural, electronic, and thermodynamic studies using ab-initio molecular dynamics calculations, showing diffusion anomaly, but no density anomaly. The origin of the transition in liquid Ti is a pressure-induced increase of local structures containing very short bonds with directionality in electronic configurations. This behavior appears to be characteristic of the early transition metals. In contrast, the late transition metal liquid Ni does not show the L-L transition with pressure. This result suggests that the possibility of the L-L transition decreases from early to late transition metals as electronic structures of late transition metals barely have a Jahn-Teller effect and bond directionality. Our results generalize that a phase transition in disordered materials is found with any valence band regardless of the sign of the melting slope, but related to the symmetry of electronic structures of constituent elements. PMID:27762334

Insights into the crystal chemistry of Earth materials rendered by electron density distributions: Pauling's rules revisited

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibbs, Gerald V.; Ross, Nancy L.; Cox, David F.

2014-05-20

Pauling's first two rules are examined in terms of the accumulation of the electron density between bonded pairs of atoms for a relatively large number of oxide and silicate crystals and siloxane molecules. The distribution of the electron density shows that the radius of the oxygen atom is not fixed, but that it actually decreases systematically from ~1.40 Å to ~ 0.65 Å as the polarizing power and the electronegativity of the bonded metal atoms increase and the distribution of the O atom is progressively polarized and contracted along the bond vectors by the impact of the bonded interactions. Themore » contractions result in an aspherical oxygen atom that displays as many different bonded “radii” as it has bonded interactions. The bonded radii for the metal atoms match the Shannon and Prewitt ionic radii for the more electropositive atoms like potassium and sodium, but they are systematically larger for the more electronegative atoms like aluminum, silicon and phosphorous. Pauling's first rule is based on the assumption that the radius of the oxide anion is fixed and that the radii of the cations are such that radius sum of the spherical oxide anion and a cation necessarily equals the separation between the cation-anion bonded pair with the coordination number of the cation being determined by the ratio of the radii of the cation and anion. In the case of the bonded radii, the sum of the bonded radii for the metal atoms and the oxide anion necessarily equals the bond lengths by virtue of the way that the bonded radii were determined in the partitioning of the electron density along the bond path into metal and O atom parts. But, the radius ratio for the O and M atoms is an unsatisfactory rule for determining the coordination number of the metal atom inasmuch as a bonded O atom is not, in general, spherical, and its size varies substantially along its bonded directions. But by counting the number of bond paths that radiate from a bonded atom, the coordination number of the atom is determined uniquely independent of the asphericity and sizes of the atom. A power law connection established between the bond lengths and bond strengths for crystals and molecules is mirrored by a comparable power law connection between bond length and the accumulation of the electron density between bonded pairs of atoms, a connection that is consistent with Pauling's electroneutrality postulate that the charges of the atoms in an oxide are negligibly small. The connection indicates that a one-to-one correspondence exists between the accumulation between a pair of bonded atoms and the Pauling bond strength for M-O bonded interaction for all atoms of the periodic table. The connection provides a common basis for understanding the success of the manifold applications that have been made with the bond valence theory model together with the modeling of crystal structures, chemical zoning, leaching and cation transport in batteries and the like. We believe that the wide spread applications of the model in mineralogy and material science owes much of its success to the direct connection between bond strength and the quantum mechanical observable, the electron density distribution. Comparable power law expressions established for the bonded interactions for both crystals and molecules support Pauling's assertion that his second rule has significance for molecules as well as for crystals. A simple expression is found that provides a one to one connection between the accumulation of the electron density between bonded M and O atoms and the Pauling bond strength for all M atoms of the periodic table with ~ 95 % of the variation of the bond strength being explained in terms of a linear dependence on the accumulated electron density. Compelling evidence is presented that supports the argument that the Si-O bonded interactions for tiny siloxane molecules and silicate crystals are chemically equivalent.« less

Gold as hydrogen: Structural and electronic properties and chemical bonding in Si3Au3+/0/- and comparisons to Si3H3+/0/-

NASA Astrophysics Data System (ADS)

Kiran, Boggavarapu; Li, Xi; Zhai, Hua-Jin; Wang, Lai-Sheng

2006-10-01

A single Au atom has been shown to behave like H in its bonding to Si in several mono- and disilicon gold clusters. In the current work, we investigate the Au /H analogy in trisilicon gold clusters, Si3Au3+/0/-. Photoelectron spectroscopy and density functional calculations are combined to examine the geometric and electronic structure of Si3Au3-. We find that there are three isomers competing for the ground state of Si3Au3- as is the case for Si3H3-. Extensive structural searches show that the potential energy surfaces of the trisilicon gold clusters (Si3Au3-, Si3Au3, and Si3Au3+) are similar to those of the corresponding silicon hydrides. The lowest energy isomers for Si3Au3- and Si3Au3 are structurally similar to a Si3Au four-membered ring serving as a common structural motif. For Si3Au3+, the 2π aromatic cyclotrisilenylium auride ion, analogous to the aromatic cyclotrisilenylium ion (Si3H3+), is the most stable species. Comparison of the structures and chemical bonding between Si3Au3+/0/- and the corresponding silicon hydrides further extends the isolobal analogy between Au and H.

Cyclo-biphenalenyl Biradicaloid Molecular Materials: Conformation, Tautomerization, Magnetism, and Thermochromism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Jingsong; Meunier, Vincent; Tian, Yong-Hui

2010-01-01

Phenalenyl and its derivatives have recently attracted a great deal of interest as a result of a two-electron multicenter (2e/mc) - bonding between two -stacked phenalenyl units. The 2e/mc bonded -dimers are close in energy to the -dimers of phenalenyl and therefore fickle properties may emerge from bond fluctuation, yielding smart -functional materials. Here, we examine the valence tautomerization of two cyclo-biphenalenyl biradicaloid molecular materials with chair and boat conformations by spin-restricted (R) and unrestricted (U) DFT using the M06 and B3LYP functionals. We found that the chair conformation involves a 2e/4c - bonded structure, whereas the boat conformation involvesmore » a 2e/12c - bonded structure on their potential energy surfaces. The global minimum for the chair conformation is the -bonded structure, whereas it is the - bonded structure for the boat conformation. The chair conformation exhibits a stepwise [3,3]-sigmatropic rearrangement, and calculations predict a negligible paramagnetic susceptibility near room temperature. In comparison, the paramagnetism of the boat conformation should be observable by SQUID and ESR. According to the energy differences of the respective - and -dimers of the two conformations and the UV-vis calculations, the color of the chair conformation is expected to become darker, whereas that of the boat conformation should become lighter with increasing temperature.« less

Bonding, moment formation, and magnetic interactions in Ca14MnBi11 and Ba14MnBi11

NASA Astrophysics Data System (ADS)

Sánchez-Portal, D.; Martin, Richard M.; Kauzlarich, S. M.; Pickett, W. E.

2002-04-01

``14-1-11'' phase compounds, based on magnetic Mn ions and typified by Ca14MnBi11 and Ba14MnBi11, show an unusual magnetic behavior, but the large number (104) of atoms in the primitive cell has precluded any previous full electronic structure study. Using an efficient, local-orbital-based method within the local-spin-density approximation to study the electronic structure, we find a gap between a bonding valence-band complex and an antibonding conduction-band continuum. The bonding bands lack one electron per formula unit of being filled, making them low carrier density p-type metals. The hole resides in the MnBi4 tetrahedral unit, and partially compensates for the high-spin d5 Mn moment, leaving a net spin near 4μB that is consistent with experiment. These manganites are composed of two disjoint but interpenetrating ``jungle gym'' networks of spin-4/2 MnBi9-4 units with ferromagnetic interactions within the same network, and weaker couplings between the networks whose sign and magnitude is sensitive to materials parameters. Ca14MnBi11 is calculated to be ferromagnetic as observed, while for Ba14MnBi11 (which is antiferromagnetic) the ferromagnetic and antiferromagnetic states are calculated to be essentially degenerate. The band structure of the ferromagnetic states is very close to half metallic.

On the ultrafast charge migration and subsequent charge directed reactivity in Cl⋯N halogen-bonded clusters following vertical ionization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chandra, Sankhabrata; Bhattacharya, Atanu, E-mail: atanub@ipc.iisc.ernet.in; Periyasamy, Ganga

2015-06-28

In this article, we have presented ultrafast charge transfer dynamics through halogen bonds following vertical ionization of representative halogen bonded clusters. Subsequent hole directed reactivity of the radical cations of halogen bonded clusters is also discussed. Furthermore, we have examined effect of the halogen bond strength on the electron-electron correlation- and relaxation-driven charge migration in halogen bonded complexes. For this study, we have selected A-Cl (A represents F, OH, CN, NH{sub 2}, CF{sub 3}, and COOH substituents) molecules paired with NH{sub 3} (referred as ACl:NH{sub 3} complex): these complexes exhibit halogen bonds. To the best of our knowledge, this ismore » the first report on purely electron correlation- and relaxation-driven ultrafast (attosecond) charge migration dynamics through halogen bonds. Both density functional theory and complete active space self-consistent field theory with 6-31 + G(d, p) basis set are employed for this work. Upon vertical ionization of NCCl⋯NH{sub 3} complex, the hole is predicted to migrate from the NH{sub 3}-end to the ClCN-end of the NCCl⋯NH{sub 3} complex in approximately 0.5 fs on the D{sub 0} cationic surface. This hole migration leads to structural rearrangement of the halogen bonded complex, yielding hydrogen bonding interaction stronger than the halogen bonding interaction on the same cationic surface. Other halogen bonded complexes, such as H{sub 2}NCl:NH{sub 3}, F{sub 3}CCl:NH{sub 3}, and HOOCCl:NH{sub 3}, exhibit similar charge migration following vertical ionization. On the contrary, FCl:NH{sub 3} and HOCl:NH{sub 3} complexes do not exhibit any charge migration following vertical ionization to the D{sub 0} cation state, pointing to interesting halogen bond strength-dependent charge migration.« less

Spectral analysis and DFT computations of the hydrogen bonded complex between 2,6-diaminopyridine with 2,6-dichloro-4-nitrophenol in different solvents

NASA Astrophysics Data System (ADS)

Al-Ahmary, Khairia M.; Soliman, Saied M.; Habeeb, Moustafa M.; Al-Obidan, Areej H.

2017-09-01

New hydrogen bonded complex between 2,6-dichloro-4-nitrophenol (DCNP), proton donor with the proton acceptor 2,6-diaminopyridine (DAP) has been synthesized and characterized in solution and solid state by different spectroscopic techniques. Electronic spectra were used to identify the novel proton transfer complex through appearance of new absorption bands in acetonitrile (CH3CN), methanol (CH3OH) and mixture composed from 1:1 methanol and acetonitrile (AN-Me). The complex stoichiometry was determined to be 1:1 by job's method and photometric titrations. The formation constant was determined by applying minimum-maximum absorbances method where it reached high values confirming the complex high stability. A spectroscopic method for determining DAP was presented and validated statistically. The solid complex was characterized by elemental analysis, infrared and 1H NMR studies where the hydrogen bonded reaction occurs between the phenolic OH with the pyridine ring nitrogen as well as one amino group of DNP. The density functional theory DFT (B3LYP) method has been used to energy optimization of the reactants and complex in the ground state using two basis sets 6-31G(d) and 6-31 G+(d,p). The first one led to energy optimized structure through bifurcated hydrogen bond between OH of DCNP with the ring nitrogen and one amino group of DAP with optimization energy -1998.7 Hartree. The second one gave an optimized structure thought hydrogen bonding between OH and one amino group with lowered optimization energy -2018.1 Hartree. Hence, the experimental results will be simulated with the most stable one at DFT/B3LYB 6-31G+ (d,p). The most reactive electrophilic and nucleophilic sites of DCNP and DAP were predicted using the molecular electrostatic potential. The theoretical electronic spectra in the gas phase and the investigated solvents were calculated at TD-DFT/B3LYP 6-31G+ (d,p) and compared with measured electronic spectra where a satisfactory results have been obtained. An important aim of this work is analysis of the interaction energies between the filled natural bond orbitals (NBOs) and the empty ones in order to shed the light on the ease of electron delocalization among bonds in the novel hydrogen bonded complex.

The active site of hen egg-white lysozyme: flexibility and chemical bonding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Held, Jeanette, E-mail: jeanette.netzel@uni-bayreuth.de; Smaalen, Sander van

Chemical bonding at the active site of lysozyme is analyzed on the basis of a multipole model employing transferable multipole parameters from a database. Large B factors at low temperatures reflect frozen-in disorder, but therefore prevent a meaningful free refinement of multipole parameters. Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader’s quantum theory of atoms in molecules [QTAIM; Bader (1994 ▶), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) ofmore » HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254–1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337–351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C—H⋯O hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.« less

Hirshfeld atom refinement for modelling strong hydrogen bonds.

PubMed

Woińska, Magdalena; Jayatilaka, Dylan; Spackman, Mark A; Edwards, Alison J; Dominiak, Paulina M; Woźniak, Krzysztof; Nishibori, Eiji; Sugimoto, Kunihisa; Grabowsky, Simon

2014-09-01

High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples of Z' > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O-H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment, e.g. the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.

A Comparative Study of Gold Bonding via Electronic Spectroscopy

NASA Astrophysics Data System (ADS)

Zhang, Ruohan

The bonding and electrostatic properties of gold containing molecules are highly influenced by relativistic effects. To understand this facet on bonding, a series of simple diatomic AuX (X=F, Cl, O and S) molecules, where upon bond formation the Au atom donates or accepts electrons, was investigated and discussed in this thesis. First, the optical field-free, Stark, and Zeeman spectroscopic studies have been performed on AuF and AuCl. The simple polar bonds between Au and typical halogens (i.e. F and Cl) can be well characterized by the electronic structure studies and the permanent electric dipole moments, mu el. The spectroscopic parameters have been precisely determined for the [17.7]1, [17.8]0+ and X1Sigma + states of AuF, and the [17.07]1, [17.20]0+ and X1Sigma+ states of AuCl. The mu el have been determined for ground and excited states of AuF and AuCl. The results from the hyperfine analysis and Stark measurement support the assignments that the [17.7]1 and [17.8]0+ states of AuF are the components of a 3pi state. Similarly, the analysis demonstrated the [19.07]1 and [19.20]0+ states are the components of the 3pi state of AuCl. Second, my study focused on AuO and AuS because the bonding between gold and sulfur/oxygen is a key component to numerous established and emerging technologies that have applications as far ranging as medical imaging, catalysis, electronics, and material science. The high-resolution spectra were record and analyzed to obtain the geometric and electronic structural data for the ground and excited states. The electric dipole moment, muel , and the magnetic dipole moment, mum, has been the precisely measured by applying external static electric and magnetic fields. muel and mum are used to give insight into the unusual complex bonding in these molecules. In addition to direct studies on the gold-containing molecules, other studies of related molecules are included here as well. These works contain the pure rotation measurement of PtC, the hyperfine and Stark spectroscopic studies of PtF, and the Stark and Zeeman spectroscopic studies of MgH and MgD. Finally, a perspective discussion and conclusion will summarize the results of AuF, AuCl, AuO, and AuS from this work (bond lengths, dipole moment, etc.). The highly quantitative information derived from this work is the foundation of a chemical description of matter and essential for kinetic energy manipulation via Stark and Zeeman interactions. This data set also establishes a synergism with computation chemists who are developing new methodologies for treating relativistic effects and electron correlation.

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer

NASA Astrophysics Data System (ADS)

Choi, Gilbert J.; Zhu, Qilei; Miller, David C.; Gu, Carol J.; Knowles, Robert R.

2016-11-01

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process—a subset of the classical Hofmann-Löffler-Freytag reaction—amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer.

PubMed

Choi, Gilbert J; Zhu, Qilei; Miller, David C; Gu, Carol J; Knowles, Robert R

2016-11-10

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process-a subset of the classical Hofmann-Löffler-Freytag reaction-amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

Quantum conductance oscillation in linear monatomic silicon chains

NASA Astrophysics Data System (ADS)

Liu, Fu-Ti; Cheng, Yan; Yang, Fu-Bin; Chen, Xiang-Rong

2014-02-01

The conductance of linear silicon atomic chains with n=1-8 atoms sandwiched between Au electrodes is investigated by using the density functional theory combined with non-equilibrium Green's function. The results show that the conductance oscillates with a period of two atoms as the number of atoms in the chain is varied. We optimize the geometric structure of nanoscale junctions in different distances, and obtain that the average bond-length of silicon atoms in each chain at equilibrium positions is 2.15±0.03 Å. The oscillation of average Si-Si bond-length can explain the conductance oscillation from the geometric structure of atomic chains. We calculate the transmission spectrum of the chains in the equilibrium positions, and explain the conductance oscillation from the electronic structure. The transport channel is mainly contributed by px and py orbital electrons of silicon atoms. The even-odd oscillation is robust under external voltage up to 1.2 V.

Controlling the Sn-C bonds content in SnO2@CNTs composite to form in situ pulverized structure for enhanced electrochemical kinetics.

PubMed

Cheng, Yayi; Huang, Jianfeng; Qi, Hui; Cao, Liyun; Luo, Xiaomin; Li, Jiayin; Xu, Zhanwei; Yang, Jun

2017-12-07

The Sn-C bonding content between the SnO 2 and CNTs interface was controlled by the hydrothermal method and subsequent heat treatment. Electrochemical analysis found that the SnO 2 @CNTs with high Sn-C bonding content exhibited much higher capacity contribution from alloying and conversion reaction compared with the low content of Sn-C bonding even after 200 cycles. The high Sn-C bonding content enabled the SnO 2 nanoparticles to stabilize on the CNTs surface, realizing an in situ pulverization process of SnO 2 . The in situ pulverized structure was beneficial to maintain the close electrochemical contact of the working electrode during the long-term cycling and provide ultrafast transfer paths for lithium ions and electrons, which promoted the alloying and conversion reaction kinetics greatly. Therefore, the SnO 2 @CNTs composite with high Sn-C bonding content displayed highly reversible alloying and conversion reaction. It is believed that the composite could be used as a reference for design chemically bonded metal oxide/carbon composite anode materials in lithium-ion batteries.

Distinct roles of a tyrosine-associated hydrogen-bond network in fine-tuning the structure and function of heme proteins: two cases designed for myoglobin.

PubMed

Liao, Fei; Yuan, Hong; Du, Ke-Jie; You, Yong; Gao, Shu-Qin; Wen, Ge-Bo; Lin, Ying-Wu; Tan, Xiangshi

2016-10-20

A hydrogen-bond (H-bond) network, specifically a Tyr-associated H-bond network, plays key roles in regulating the structure and function of proteins, as exemplified by abundant heme proteins in nature. To explore an approach for fine-tuning the structure and function of artificial heme proteins, we herein used myoglobin (Mb) as a model protein and introduced a Tyr residue in the secondary sphere of the heme active site at two different positions (107 and 138). We performed X-ray crystallography, UV-Vis spectroscopy, stopped-flow kinetics, and electron paramagnetic resonance (EPR) studies for the two single mutants, I107Y Mb and F138Y Mb, and compared to that of wild-type Mb under the same conditions. The results showed that both Tyr107 and Tyr138 form a distinct H-bond network involving water molecules and neighboring residues, which fine-tunes ligand binding to the heme iron and enhances the protein stability, respectively. Moreover, the Tyr107-associated H-bond network was shown to fine-tune both H2O2 binding and activation. With two cases demonstrated for Mb, this study suggests that the Tyr-associated H-bond network has distinct roles in regulating the protein structure, properties and functions, depending on its location in the protein scaffold. Therefore, it is possible to design a Tyr-associated H-bond network in general to create other artificial heme proteins with improved properties and functions.

Bonding structure in amorphous carbon nitride: A spectroscopic and nuclear magnetic resonance study

NASA Astrophysics Data System (ADS)

Sánchez-López, J. C.; Donnet, C.; Lefèbvre, F.; Fernández-Ramos, C.; Fernández, A.

2001-07-01

Since the prediction of Liu and Cohen [Science 245, 841 (1989)] of the potential extraordinary mechanical properties of crystalline β-C3N4, many authors have attempted its synthesis. However, in most cases, the obtained materials are amorphous phases with a complex bonding structure. Their characterization is complicated due to the absence of a reference compound, the lack of long-range order, and the poor knowledge about their bonding structure. In this article, we present 1H, 13C, and 15N solid-state nuclear magnetic resonance (NMR) measurements for the determination of the bonding types in amorphous CNx films. NMR measurements do not require long-range order and are able to clearly identify the signals from the sp2- and sp3-bonded phases. The analysis of the data obtained by other characterization techniques, such as infrared spectroscopy, x-ray photoelectron spectroscopy, electron energy-loss spectroscopy, and x-ray absorption near-edge spectroscopy on the same sample, based on the information acquired by NMR, enables the description of a structure model for the studied amorphous-CNx phase prepared by dc-magnetron sputtering and to revise the interpretation found in the literature.

Implication of the solvent effect, metal ions and topology in the electronic structure and hydrogen bonding of human telomeric G-quadruplex DNA.

PubMed

Poudel, Lokendra; Steinmetz, Nicole F; French, Roger H; Parsegian, V Adrian; Podgornik, Rudolf; Ching, Wai-Yim

2016-08-03

We present a first-principles density functional study elucidating the effects of solvent, metal ions and topology on the electronic structure and hydrogen bonding of 12 well-designed three dimensional G-quadruplex (G4-DNA) models in different environments. Our study shows that the parallel strand structures are more stable in dry environments and aqueous solutions containing K(+) ions within the tetrad of guanine but conversely, that the anti-parallel structure is more stable in solutions containing the Na(+) ions within the tetrad of guanine. The presence of metal ions within the tetrad of the guanine channel always enhances the stability of the G4-DNA models. The parallel strand structures have larger HOMO-LUMO gaps than antiparallel structures, which are in the range of 0.98 eV to 3.11 eV. Partial charge calculations show that sugar and alkali ions are positively charged whereas nucleobases, PO4 groups and water molecules are all negatively charged. Partial charges on each functional group with different signs and magnitudes contribute differently to the electrostatic interactions involving G4-DNA and favor the parallel structure. A comparative study between specific pairs of different G4-DNA models shows that the Hoogsteen OH and NH hydrogen bonds in the guanine tetrad are significantly influenced by the presence of metal ions and water molecules, collectively affecting the structure and the stability of G4-DNA.

Covalent lanthanide(III) macrocyclic complexes: the bonding nature and optical properties of a promising single antenna molecule.

PubMed

Rabanal-León, Walter A; Páez-Hernández, Dayán; Arratia-Pérez, Ramiro

2014-12-21

The present work is focused on the elucidation of the electronic structure, bonding nature and optical properties of a series of low symmetry (C2) coordination compounds of type [Ln(III)HAM](3+), where "Ln(III)" are the trivalent lanthanide ions: La(3+), Ce(3+), Eu(3+) and Lu(3+), while "HAM" is the neutral six-nitrogen donor macrocyclic ligand [C22N6H26]. This systematic study has been performed in the framework of the Relativistic Density Functional Theory (R-DFT) and also using a multi-reference approach via the Complete Active Space (CAS) wavefunction treatment with the aim of analyzing their ground state and excited state electronic structures as well as electronic correlation. Furthermore, the use of the energy decomposition scheme proposed by Morokuma-Ziegler and the electron localization function (ELF) allows us to characterize the bonding between the lanthanide ions and the macrocyclic ligand, obtaining as a result a dative-covalent interaction. Due to a great deal of lanthanide optical properties and their technological applications, the absorption spectra of this set of coordination compounds were calculated using the time-dependent density functional theory (TD-DFT), where the presence of the intense Ligand to Metal Charge Transfer (LMCT) bands in the ultraviolet and visible region and the inherent f-f electronic transitions in the Near-Infra Red (NIR) region for some lanthanide ions allow us to propose these systems as "single antenna molecules" with potential applications in NIR technologies.

Structure and bonding in beta-HMX-characterization of a trans-annular N...N interaction.

PubMed

Zhurova, Elizabeth A; Zhurov, Vladimir V; Pinkerton, A Alan

2007-11-14

Chemical bonding in the beta-phase of the 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX) crystal based on the experimental electron density obtained from X-ray diffraction data at 20 K, and solid state theoretical calculations, has been analyzed in terms of the quantum theory of atoms in molecules. Features of the intra- and intermolecular bond critical points and the oxygen atom lone-pair locations are discussed. An unusual N...N bonding interaction across the 8-membered ring has been discovered and characterized. Hydrogen bonding, O...O and O...C intermolecular interactions are reported. Atomic charges and features of the electrostatic potential are discussed.

``Making the Molecular Movie'': First Frames

NASA Astrophysics Data System (ADS)

Miller, R. J. Dwayne

2011-03-01

Femtosecond Electron Diffraction has enabled atomic resolution to structural changes as they occur, essentially watching atoms move in real time--directly observe transition states. This experiment has been referred to as ``making the molecular movie'' and has been previously discussed in the context of a gedanken experiment. With the recent development of femtosecond electron pulses with sufficient number density to execute single shot structure determinations, this experiment has been finally realized. A new concept in electron pulse generation was developed based on a solution to the N-body electron propagation problem involving up to 10,000 interacting electrons that has led to a new generation of extremely bright electron pulsed sources that minimizes space charge broadening effects. Previously thought intractable problems of determining t=0 and fully characterizing electron pulses on the femtosecond time scale have now been solved through the use of the laser pondermotive potential to provide a time dependent scattering source. Synchronization of electron probe and laser excitation pulses is now possible with an accuracy of 10 femtoseconds to follow even the fastest nuclear motions. The camera for the ``molecular movie'' is well in hand based on high bunch charge electron sources. Several movies depicting atomic motions during passage through structural transitions will be shown. Atomic level views of the simplest possible structural transition, melting, will be presented for a number of systems in which both thermal and purely electronically driven atomic displacements can be correlated to the degree of directional bonding. Optical manipulation of charge distributions and effects on interatomic forces/bonding can be directly observed through the ensuing atomic motions. New phenomena involving strongly correlated electron systems will be presented in which an exceptionally cooperative phase transitions has been observed. The primitive origin of molecular cooperativity has also been discovered in recent studies of molecular crystals. These new developments will be discussed in the context of developing the necessary technology to directly observe the structure-function correlation in biomolecules--the fundamental molecular basis of biological systems.

Electron density determination and bonding in tetragonal binary intermetallics by convergent beam electron diffraction

NASA Astrophysics Data System (ADS)

Sang, Xiahan

Intermetallics offer unique property combinations often superior to those of more conventional solid solution alloys of identical composition. Understanding of bonding in intermetallics would greatly accelerate development of intermetallics for advanced and high performance engineering applications. Tetragonal intermetallics L10 ordered TiAl, FePd and FePt are used as model systems to experimentally measure their electron densities using quantitative convergent beam electron diffraction (QCBED) method and then compare details of the 3d-4d (FePd) and 3d-5d (FePt) electron interactions to elucidate their role on properties of the respective ferromagnetic L10-ordered intermetallics FePd and FePt. A new multi-beam off-zone axis condition QCBED method has been developed to increase sensitivity of CBED patterns to change of structure factors and the anisotropic Debye-Waller (DW) factors. Unprecedented accuracy and precision in structure and DW factor measurements has been achieved by acquiring CBED patterns using beam-sample geometry that ensures strong dynamical interaction between the fast electrons and the periodic potential in the crystalline samples. This experimental method has been successfully applied to diamond cubic Si, and chemically ordered B2 cubic NiAl, tetragonal L10 ordered TiAl and FePd. The accurate and precise experimental DW and structure factors for L10 TiAl and FePd allow direct evaluation of computer calculations using the current state of the art density functional theory (DFT) based electron structure modeling. The experimental electron density difference map of L1 0 TiAl shows that the DFT calculations describe bonding to a sufficient accuracy for s- and p- electrons interaction, e. g., the Al-layer. However, it indicate significant quantitative differences to the experimental measurements for the 3d-3d interactions of the Ti atoms, e.g. in the Ti layers. The DFT calculations for L10 FePd also show that the current DFT approximations insufficiently describe the interaction between Fe-Fe (3d-3d), Fe-Pd (3d-4d) and Pd-Pd (4d-4d) electrons, which indicates the necessity to evaluate applicability of different DFT approximations, and also provides experimental data for the development of new DFT approximation that better describes transition metal based intermetallic systems.

Understanding the fast phase-change mechanism of tetrahedrally bonded Cu2GeTe3 : Comprehensive analyses of electronic structure and transport phenomena

NASA Astrophysics Data System (ADS)

Kobayashi, Keisuke; Skelton, Jonathan M.; Saito, Yuta; Shindo, Satoshi; Kobata, Masaaki; Fons, Paul; Kolobov, Alexander V.; Elliott, Stephen; Ando, Daisuke; Sutou, Yuji

2018-05-01

Cu2GeTe3 (CGT) phase-change material, a promising candidate for advanced fast nonvolatile random-access-memory devices, has a chalcopyritelike structure with s p3 bonding in the crystalline phase; thus, the phase-change (PC) mechanism is considered to be essentially different from that of the standard PC materials (e.g., Ge-Sb-Te) with threefold to sixfold p -like bonding. In order to reveal the PC mechanism of CGT, the electronic structure change due to PC has been investigated by laboratory hard x-ray photoelectron spectroscopy and combined first-principles density-functional theory molecular-dynamics simulations. The valence-band spectra, in both crystalline and amorphous phases, are well simulated by the calculations. An inherent tendency of Te 5 s lone-pair formation and an enhanced participation of Cu 3 d orbitals in the bonding are found to play dominant roles in the PC mechanism. The electrical conductivity of as-deposited films and its change during the PC process is investigated in connection with valence-band spectral changes near the Fermi level. The results are successfully analyzed, based on a model proposed by Davis and Mott for chalcogenide amorphous semiconductors. The results suggest that robustness of the defect-band states against thermal stress is a key to the practical application of this material for memory devices.

Study of first electronic transition and hydrogen bonding state of ultra-thin water layer of nanometer thickness on an α-alumina surface by far-ultraviolet spectroscopy

NASA Astrophysics Data System (ADS)

Goto, Takeyoshi; Kinugasa, Tomoya

2018-05-01

The first electronic transition (A˜ ← X˜) and the hydrogen bonding state of an ultra-thin water layer of nanometer thickness between two α-alumina surfaces (0.5-20 nm) were studied using far-ultraviolet (FUV) spectroscopy in the wavelength range 140-180 nm. The ultra-thin water layer of nanometer thickness was prepared by squeezing a water droplet ( 1 μL) between a highly polished α-alumina prism and an α-alumina plate using a high pressure clamp ( 4.7 MPa), and the FUV spectra of the water layer at different thicknesses were measured using the attenuated total reflection method. As the water layer became thinner, the A˜ ← X˜ bands were gradually shifted to higher or lower energy relative to that of bulk water; at thicknesses smaller than 4 nm, these shifts were substantial (0.1-0.2 eV) in either case. The FUV spectra of the water layer with thickness < 4 nm indicate the formation of structured ice-like hydrogen bond (H-bond) layers for the higher energy shifts or the formation of slightly weaker H-bond layers as compared to those in the bulk liquid state for lower energy shifts. In either case, the H-bond structure of bulk liquid water is nearly lost at thicknesses below 4 nm, because of steric hydration forces between the α-alumina surfaces.

Facile fabrication of high-performance InGaZnO thin film transistor using hydrogen ion irradiation at room temperature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahn, Byung Du; Park, Jin-Seong; Chung, K. B., E-mail: kbchung@dongguk.edu

Device performance of InGaZnO (IGZO) thin film transistors (TFTs) are investigated as a function of hydrogen ion irradiation dose at room temperature. Field effect mobility is enhanced, and subthreshold gate swing is improved with the increase of hydrogen ion irradiation dose, and there is no thermal annealing. The electrical device performance is correlated with the electronic structure of IGZO films, such as chemical bonding states, features of the conduction band, and band edge states below the conduction band. The decrease of oxygen deficient bonding and the changes in electronic structure of the conduction band leads to the improvement of devicemore » performance in IGZO TFT with an increase of the hydrogen ion irradiation dose.« less

Evaluation of antioxidant activity and electronic structure of aspirin and paracetamol

NASA Astrophysics Data System (ADS)

Motozaki, W.; Nagatani, Y.; Kimura, Y.; Endo, K.; Takemura, T.; Kurmaev, E. Z.; Moewes, A.

2011-01-01

We present a study of electronic structure, chemical bonding, and antioxidant activity of phenolic antioxidants (aspirin and paracetamol). X-ray photoelectron and emission spectra of the antioxidants have been simulated by deMon density functional theory (DFT) calculations of the molecules. The chemical bonding of aspirin is characterized by the formation of oxygen 'lone-pair' π-orbitals which can neutralize free radicals and thus be related to antioxidant properties of the drug. In the case of paracetamol the additional nitrogen 'lone pair' is formed which can explain toxicity of the drug. We propose an evaluation method of antioxidant activity based on the relationship between experimental half-wave oxidation potential ( Ep/2 ) and calculated ionization potentials ( IP) by the DFT calculations, and can conclude that paracetamol has the higher antioxidant activity than aspirin.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, Amrish, E-mail: amrish99@gmail.com; Kaur, Sandeep, E-mail: sipusukhn@gmail.com; Mudahar, Isha, E-mail: isha@pbi.ac.in

We have investigated the structural and electronic properties of carbon nanotube with small fullerene halves C{sub n} (n ≤ 40) which are covalently bonded to the side wall of an armchair single wall carbon nanotube (SWCNT) using first principle method based on density functional theory. The fullerene size results in weak bonding between fullerene halves and carbon nanotube (CNT). Further, it was found that the C-C bond distance that attaches the fullerene half and CNT is of the order of 1.60 Å. The calculated binding energies indicate the stability of the complexes formed. The HOMO-LUMO gaps and electron density ofmore » state plots points towards the metallicity of the complex formed. Our calculations on charge transfer reveal that very small amount of charge is transferred from CNT to fullerene halves.« less

Probing the structural and dynamical properties of liquid water with models including non-local electron correlation

NASA Astrophysics Data System (ADS)

Del Ben, Mauro; Hutter, Jürg; VandeVondele, Joost

2015-08-01

Water is a ubiquitous liquid that displays a wide range of anomalous properties and has a delicate structure that challenges experiment and simulation alike. The various intermolecular interactions that play an important role, such as repulsion, polarization, hydrogen bonding, and van der Waals interactions, are often difficult to reproduce faithfully in atomistic models. Here, electronic structure theories including all these interactions at equal footing, which requires the inclusion of non-local electron correlation, are used to describe structure and dynamics of bulk liquid water. Isobaric-isothermal (NpT) ensemble simulations based on the Random Phase Approximation (RPA) yield excellent density (0.994 g/ml) and fair radial distribution functions, while various other density functional approximations produce scattered results (0.8-1.2 g/ml). Molecular dynamics simulation in the microcanonical (NVE) ensemble based on Møller-Plesset perturbation theory (MP2) yields dynamical properties in the condensed phase, namely, the infrared spectrum and diffusion constant. At the MP2 and RPA levels of theory, ice is correctly predicted to float on water, resolving one of the anomalies as resulting from a delicate balance between van der Waals and hydrogen bonding interactions. For several properties, obtaining quantitative agreement with experiment requires correction for nuclear quantum effects (NQEs), highlighting their importance, for structure, dynamics, and electronic properties. A computed NQE shift of 0.6 eV for the band gap and absorption spectrum illustrates the latter. Giving access to both structure and dynamics of condensed phase systems, non-local electron correlation will increasingly be used to study systems where weak interactions are of paramount importance.

Structure of selected basic zinc/copper (II) phosphate minerals based upon near-infrared spectroscopy--implications for hydrogen bonding.

PubMed

Frost, Ray L; Reddy, B Jagannadha; Palmer, Sara J; Keeffe, Eloise C

2011-03-01

The NIR spectra of reichenbachite, scholzite and parascholzite have been studied at 298 K. The spectra of the minerals are different, in line with composition and crystal structural variations. Cation substitution effects are significant in their electronic spectra and three distinctly different electronic transition bands are observed in the near-infrared spectra at high wavenumbers in the 12,000-7600 cm(-1) spectral region. Reichenbachite electronic spectrum is characterised by Cu(II) transition bands at 9755 and 7520 cm(-1). A broad spectral feature observed for ferrous ion in the 12,000-9000 cm(-1) region both in scholzite and parascholzite. Some what similarities in the vibrational spectra of the three phosphate minerals are observed particularly in the OH stretching region. The observation of strong band at 5090 cm(-1) indicates strong hydrogen bonding in the structure of the dimorphs, scholzite and parascholzite. The three phosphates exhibit overlapping bands in the 4800-4000 cm(-1) region resulting from the combinations of vibrational modes of (PO(4))(3-) units. Copyright © 2010 Elsevier B.V. All rights reserved.

Synthesis, crystal structure and DFT studies of a dual fluorescent ketamine: Structural changes in the ground and excited states

NASA Astrophysics Data System (ADS)

Latha, V.; Balakrishnan, C.; Neelakantan, M. A.

2015-07-01

A fluorescent probe 2Z,2‧Z-3,3‧-(4,4‧-methylenebis(4,1-phenylene) bis(azanediyl))bis (1,3-diphenylprop-2-en-1-one) (L) was synthesized and characterized by IR, 1H NMR, ESI-mass, UV-visible and fluorescence spectral techniques. The single crystal analysis illustrates the existence of L in ketamine form. The crystal structure is stabilized by intramolecular and intermolecular hydrogen bonding. The thermal stability of L was studied by TG analysis. The fluorescence spectrum of L shows dual emission, and is due to excited state intramolecular proton transfer (ESIPT) process. This is supported by the high Stokes shift value. Electronic structure calculations of L in the ground and excited state have been carried out using DFT and TD-DFT at B3LYP/6-31G (d,p) level, respectively. The vibrational spectrum was computed at this level and compared with experimental values. Major orbital contributions for the electronic transitions were assigned with the help of TD-DFT. The changes in the Mulliken charge, bond lengths and bond angles between the ground and excited states of the tautomers demonstrate that twisted intramolecular charge transfer (TICT) process occurs along with ESIPT in the excited state.

The effect of nitrogen incorporation on the bonding structure of hydrogenated carbon nitride films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Camero, M.; Buijnsters, J. G.; Gomez-Aleixandre, C.

2007-03-15

This work describes the composition and bonding structure of hydrogenated carbon nitride (a-CN{sub x}:H) films synthesized by electron cyclotron resonance chemical vapor deposition using as precursor gases argon, methane, and nitrogen. The composition of the films was derived from Rutherford backscattering and elastic recoil detection analysis and the bonding structure was examined by infrared (IR) spectroscopy and x-ray absorption near edge spectroscopy (XANES). By varying the nitrogen to methane ratio in the applied gas mixture, polymeric a-CN{sub x}:H films with N/C contents varying from 0.06 to 0.49 were obtained. Remarkably, the H content of the films ({approx}40 at. %) wasmore » rather unaffected by the nitrogenation process. The different bonding states as detected in the measured XANES C(1s) and N(1s) spectra have been correlated with those of a large number of reference samples. The XANES and IR spectroscopy results indicate that N atoms are efficiently incorporated into the amorphous carbon network and can be found in different bonding environments, such as pyridinelike, graphitelike, nitrilelike, and amino groups. The nitrogenation of the films results in the formation of N-H bonding environments at the cost of C-H structures. Also, the insertion of N induces a higher fraction of double bonds in the structure at the expense of the linear polymerlike chains, hence resulting in a more cross-linked solid. The formation of double bonds takes place through complex C=N structures and not by formation of graphitic aromatic rings. Also, the mechanical and tribological properties (hardness, friction, and wear) of the films have been studied as a function of the nitrogen content. Despite the major modifications in the bonding structure with nitrogen uptake, no significant changes in these properties are observed.« less

Recent advances in aerospace composite NDE

NASA Astrophysics Data System (ADS)

Georgeson, Gary E.

2002-06-01

As the aerospace industry continues to advance the design and use of composite structure, the NDE community faces the difficulties of trying to keep up. The challenges lie in manufacturing evaluation of the newest aerospace structures and materials and the in-service inspection and monitoring of damaged or aging composites. This paper provides examples of several promising NDI applications in the world of aerospace composites. Airborne (or non-contact) Ultrasonic Testing (UT) has been available for decades, but recently has generated new interest due to significant improvements in transducer design and low noise electronics. Boeing is developing inspection techniques for composite joints and core blankets using this technology. In-service inspection techniques for thick, multi-layer structures are also being advanced. One effective technique integrates the S-9 Sondicator, a traditional bond testing device, with Boeing's Mobile Automated Scanner (MAUS) platform. Composite patches have seen limited use on-aircraft, due, in part, to the difficulty of determining the quality of a bonded joint. A unique approach using Electronic Speckle Pattern Interferometry (ESPI) is showing promise as a bonded patch-inspection method. Other NDI techniques currently being developed for aerospace application are also briefly discussed.

A theory for bioinorganic chemical reactivity of oxometal complexes and analogous oxidants: the exchange and orbital-selection rules.

PubMed

Usharani, Dandamudi; Janardanan, Deepa; Li, Chunsen; Shaik, Sason

2013-02-19

Over the past decades metalloenzymes and their synthetic models have emerged as an area of increasing research interest. The metalloenzymes and their synthetic models oxidize organic molecules using oxometal complexes (OMCs), especially oxoiron(IV)-based ones. Theoretical studies have helped researchers to characterize the active species and to resolve mechanistic issues. This activity has generated massive amounts of data on the relationship between the reactivity of OMCs and the transition metal's identity, oxidation state, ligand sphere, and spin state. Theoretical studies have also produced information on transition state (TS) structures, reaction intermediates, barriers, and rate-equilibrium relationships. For example, the experimental-theoretical interplay has revealed that nonheme enzymes carry out H-abstraction from strong C-H bonds using high-spin (S = 2) oxoiron(IV) species with four unpaired electrons on the iron center. However, other reagents with higher spin states and more unpaired electrons on the metal are not as reactive. Still other reagents carry out these transformations using lower spin states with fewer unpaired electrons on the metal. The TS structures for these reactions exhibit structural selectivity depending on the reactive spin states. The barriers and thermodynamic driving forces of the reactions also depend on the spin state. H-Abstraction is preferred over the thermodynamically more favorable concerted insertion into C-H bonds. Currently, there is no unified theoretical framework that explains the totality of these fascinating trends. This Account aims to unify this rich chemistry and understand the role of unpaired electrons on chemical reactivity. We show that during an oxidative step the d-orbital block of the transition metal is enriched by one electron through proton-coupled electron transfer (PCET). That single electron elicits variable exchange interactions on the metal, which in turn depend critically on the number of unpaired electrons on the metal center. Thus, we introduce the exchange-enhanced reactivity (EER) principle, which predicts the preferred spin state during oxidation reactions, the dependence of the barrier on the number of unpaired electrons in the TS, and the dependence of the deformation energy of the reactants on the spin state. We complement EER with orbital-selection rules, which predict the structure of the preferred TS and provide a handy theory of bioinorganic oxidative reactions. These rules show how EER provides a Hund's Rule for chemical reactivity: EER controls the reactivity landscape for a great variety of transition-metal complexes and substrates. Among many reactivity patterns explained, EER rationalizes the abundance of high-spin oxoiron(IV) complexes in enzymes that carry out bond activation of the strongest bonds. The concepts used in this Account might also be applicable in other areas such as in f-block chemistry and excited-state reactivity of 4d and 5d OMCs.

Role of Electronic Structure In Ion Band State Theory of Low Energy Nuclear Reactions

NASA Astrophysics Data System (ADS)

Chubb, Scott

2004-03-01

The Nuts and Bolts of our Ion Band State (IBS) theory of low energy nuclear reactions (LENR's) in palladium-deuteride (PdD) and palladium-hydride (PdH) are the electrons that hold together or tear apart the bonds (or lack of bonds) between deuterons (d's) or protons (p's) and the host material. In PdDx and PdH_x, this bonding is strongly correlated with loading: in ambient loading conditions (x< 0. 6), the bonding in hibits IBS occupation. As x arrow 1, slight increases and decreases in loading can lead to vibrations (which have conventionally been thought to occur from phonons) that can induce potential losses or increases of p/d. Naive assumptions about phonons fail to include these losses and increases. These effects can occur because neither H or D has core electrons and because in either PdD or PdH, the electrons near the Fermi Energy have negligible overlap with the nucleus of either D or H. I use these ideas to develop a formal justification, based on a generalization of conventional band theory (Scott Chubb, "Semi-Classical Conduction of Charged and Neutral Particles in Finite Lattices," 2004 March Meeting."), for the idea that occupation of IBS's can occur and that this can lead to nuclear reactions.

Mechanism of aquaporin-4's fast and highly selective water conduction and proton exclusion.

PubMed

Tani, Kazutoshi; Mitsuma, Tadanori; Hiroaki, Yoko; Kamegawa, Akiko; Nishikawa, Kouki; Tanimura, Yukihiro; Fujiyoshi, Yoshinori

2009-06-19

Members of the aquaporin (AQP) family are expressed in almost every organism, including 13 homologues in humans. Based on the electron crystallographic structure of AQP1, the hydrogen-bond isolation mechanism was proposed to explain why AQPs are impermeable to protons despite their very fast water conduction. The mechanism by which AQPs exclude protons remained controversial, however. Here we present the structure of AQP4 at 2.8 A resolution obtained by electron crystallography of double-layered two-dimensional crystals. The resolution has been improved from the previous 3.2 A, with accompanying improvement in data quality resulting in the ability to identify individual water molecules. Our structure of AQP4, the predominant water channel in the brain, reveals eight water molecules in the channel. The arrangement of the waters provides support for the hydrogen-bond isolation mechanism. Our AQP4 structure also visualizes five lipids, showing that direct interactions of the extracellular surface of AQP4 with three lipids in the adjoining membrane help stabilize the membrane junction.

Velocity modulation spectroscopy of molecular ions II: The millimeter/submillimeter-wave spectrum of TiF + ( X3Φr)

NASA Astrophysics Data System (ADS)

Halfen, D. T.; Ziurys, L. M.

2006-11-01

The pure rotational spectrum of the molecular ion TiF + in its 3Φr ground state has been measured in the range 327-542 GHz using millimeter-wave direct absorption techniques combined with velocity modulation spectroscopy. TiF + was made in an AC discharge from a mixture of TiCl 4, F 2 in He, and argon. Ten transitions of this ion were recorded. In every transition, fluorine hyperfine interactions, as well as the fine structure splittings, were resolved. The fine structure pattern was found to be regular with almost equal spacing in frequency between the three spin components, in contrast to TiCl +, which is perturbed in the ground state. The data were fit with a case ( a) Hamiltonian and rotational, fine structure, and hyperfine constants were determined. The bond length established for TiF +, r0 = 1.7775 Å, was found to be shorter than that of TiF, r0 = 1.8342 Å—also established from mm-wave data. The hyperfine parameters determined are consistent with a δ1π1 electron configuration with the electrons primarily located on the titanium nucleus. The nuclear spin-orbit constant a indicates that the unpaired electrons are closer to the fluorine nucleus in TiF + relative to TiF, as expected with the decrease in bond length for the ion. The shorter bond distance is thought to arise from increased charge on the titanium nucleus as a result of a Ti 2+F - configuration. A similar decrease in bond length was found for TiCl + relative to TiCl.

NASA Astrophysics Data System (ADS)

Yao, Jinhuan; Li, Yanwei; Li, Xuanhai; Le, Shiru

2014-07-01

The geometric structure, electronic structure, and stability of In-substituted ZnFe2O4 (Zn7InFe16O32 and Zn8Fe15InO32) are investigated by the density functional theory at generalized gradient approximation level. Compared with the perfect ZnFe2O4 (Zn8Fe16O32), the unit cell volume of In-substituted ZnFe2O4 increases and the structure deforms slightly. The formation energy of In substitution for Zn is smaller than that of In substitution for Fe, indicating that Zn7InFe16O32 is easier to be formed than Zn8Fe15InO32. In substitution changes the properties of ZnFe2O4 from semiconducting character to metallic character. For ZnFe2O4 and In-substituted ZnFe2O4, the strength of O-Zn bond is stronger than O-Fe bond and both of them have a covalent bond character. The strength of O-In bond is similar to that of O-Zn bond in Zn7InFe16O32, but weaker than O-Fe in Zn8Fe15InO32. In substitution for Zn causes the strength of O-Fe bonds around In atom to weaken. In substitution for Fe causes the strength of O-Zn bonds around In atom to weaken obviously, while the strength of O-Fe bonds strengthen slightly.

Large space systems technology electronics: Data and power distribution

NASA Technical Reports Server (NTRS)

Dunbar, W. G.

1980-01-01

The development of hardware technology and manufacturing techniques required to meet space platform and antenna system needs in the 1980s is discussed. Preliminary designs for manned and automatically assembled space power system cables, connectors, and grounding and bonding materials and techniques are reviewed. Connector concepts, grounding design requirements, and bonding requirements are discussed. The problem of particulate debris contamination for large structure spacecraft is addressed.

Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations.

PubMed

Radhika, R; Shankar, R; Vijayakumar, S; Kolandaivel, P

2018-05-01

The theoretical studies on DNA with the anticancer drug 6-Mercaptopurine (6-MP) are investigated using theoretical methods to shed light on drug designing. Among the DNA base pairs considered, 6-MP is stacked with GC with the highest interaction energy of -46.19 kcal/mol. Structural parameters revealed that structure of the DNA base pairs is deviated from the planarity of the equilibrium position due to the formation of hydrogen bonds and stacking interactions with 6-MP. These deviations are verified through the systematic comparison between X-H bond contraction and elongation and the associated blue shift and red shift values by both NBO analysis and vibrational analysis. Bent's rule is verified for the C-H bond contraction in the 6-MP interacted base pairs. The AIM results disclose that the higher values of electron density (ρ) and Laplacian of electron density (∇ 2 ρ) indicate the increased overlap between the orbitals that represent the strong interaction and positive values of the total electron density show the closed-shell interaction. The relative sensitivity of the chemical shift values for the DNA base pairs with 6-MP is investigated to confirm the hydrogen bond strength. Molecular dynamics simulation studies of G-quadruplex DNA d(TGGGGT) 4 with 6-MP revealed that the incorporation of 6-MP appears to cause local distortions and destabilize the G-quadruplex DNA.

Polarizable atomic multipole X-ray refinement: application to peptide crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schnieders, Michael J.; Fenn, Timothy D.; Howard Hughes Medical Institute

2009-09-01

A method to accelerate the computation of structure factors from an electron density described by anisotropic and aspherical atomic form factors via fast Fourier transformation is described for the first time. Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussianmore » multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of interatomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA–IAS model lowered R{sub free} by 20–40% relative to the original spherically symmetric scattering model.« less

Electron transport in NH3/NO2 sensed buckled antimonene

NASA Astrophysics Data System (ADS)

Srivastava, Anurag; Khan, Md. Shahzad; Ahuja, Rajeev

2018-04-01

The structural and electronic properties of buckled antimonene have been analysed using density functional theory based ab-initio approach. Geometrical parameters in terms of bond length and bond angle are found close to the single ruffle mono-layer of rhombohedral antimony. Inter-frontier orbital analyses suggest localization of lone pair electrons at each atomic centre. Phonon dispersion along with high symmetry point of Brillouin zone does not signify any soft mode. With an electronic band gap of 1.8eV, the quasi-2D nano-surface has been further explored for NH3/NO2 molecules sensing and qualities of interaction between NH3/NO2 gas and antimonene scrutinized in terms of electronic charges transfer. A current-voltage characteristic has also been analysed, using Non Equilibrium Green's function (NEGF), for antimonene, in presence of incoming NH3/NO2 molecules.

Salt-Assisted Ultrasonicated De-Aggregation and Advanced Redox Electrochemistry of Detonation Nanodiamond

PubMed Central

Gupta, Sanju; Evans, Brendan; Henson, Alex; Carrizosa, Sara B.

2017-01-01

Nanodiamond particles form agglomerates in the dry powder state and this poses limitation to the accessibility of their diamond-like core thus dramatically impacting their technological advancement. In this work, we report de-agglomeration of nanodiamond (ND) by using a facile technique namely, salt-assisted ultrasonic de-agglomeration (SAUD). Utilizing ultrasound energy and ionic salts (sodium chloride and sodium acetate), SAUD is expected to break apart thermally treated nanodiamond aggregates (~50–100 nm) and produce an aqueous slurry of de-aggregated stable colloidal nanodiamond dispersions by virtue of ionic interactions and electrostatic stabilization. Moreover, the SAUD technique neither has toxic chemicals nor is it difficult to remove impurities and therefore the isolated nanodiamonds produced are exceptionally suited for engineered nanocarbon for mechanical (composites, lubricants) and biomedical (bio-labeling, biosensing, bioimaging, theranostic) applications. We characterized the microscopic structure using complementary techniques including transmission electron microscopy combined with selected-area electron diffraction, optical and vibrational spectroscopy. We immobilized SAUD produced NDs on boron-doped diamond electrodes to investigate fundamental electrochemical properties. They included surface potential (or Fermi energy level), carrier density and mapping electrochemical (re)activity using advanced scanning electrochemical microscopy in the presence of a redox-active probe, with the aim of understanding the surface redox chemistry and the interfacial process of isolated nanodiamond particles as opposed to aggregated and untreated nanoparticles. The experimental findings are discussed in terms of stable colloids, quantum confinement and predominantly surface effects, defect sites (sp2–bonded C and unsaturated bonds), inner core (sp3–bonded C)/outer shell (sp2–bonded C) structure, and surface functionality. Moreover, the surface electronic states give rise to midgap states which serve as electron donors (or acceptors) depending upon the bonding (or antibonding). These are important as electroanalytical platforms for various electrocatalytic processes. PMID:29125547

Symmetry and electronic structure of noble-metal nanoparticles and the role of relativity.

PubMed

Häkkinen, Hannu; Moseler, Michael; Kostko, Oleg; Morgner, Nina; Hoffmann, Margarita Astruc; von Issendorff, Bernd

2004-08-27

We present high resolution UV-photoelectron spectra of cold mass selected Cun-, Agn-, and Aun- with n=53-58. The observed electron density of states is not the expected simple electron shell structure, but is strongly influenced by electron-lattice interactions. Only Cu55- and Ag55- exhibit highly degenerate states. This is a direct consequence of their icosahedral symmetry, as is confirmed by density functional theory calculations. Neighboring sizes exhibit perturbed electronic structures, as they are formed by removal or addition of atoms to the icosahedron and therefore have lower symmetries. Gold clusters in the same size range show completely different spectra with almost no degeneracy, which indicates that they have structures of much lower symmetry. This behavior is related to strong relativistic bonding effects in gold, as demonstrated by ab initio calculations for Au55-.

A Diamond Electron Tunneling Micro-Electromechanical Sensor

NASA Technical Reports Server (NTRS)

Albin, Sacharia

2000-01-01

A new pressure sensing device using field emission from diamond coated silicon tips has been developed. A high electric field applied between a nano-tip array and a diaphragm configured as electrodes produces electron emission governed by the Fowler Nordheim equation. The electron emission is very sensitive to the separation between the diaphragm and the tips, which is fixed at an initial spacing and bonded such that a cavity is created between them. Pressure applied to the diaphragm decreases the spacing between the electrodes, thereby increasing the number of electrons emitted. Silicon has been used as a substrate on which arrays of diamond coated sharp tips have been fabricated for electron emission. Also, a diaphragm has been made using wet orientation dependent etching. These two structures were bonded together using epoxy and tested. Current - voltage measurements were made at varying pressures for 1-5 V biasing conditions. The sensitivity was found to be 2.13 mV/V/psi for a 20 x 20 array, which is comparable to that of silicon piezoresistive transducers. Thinner diaphragms as well as alternative methods of bonding are expected to improve the electrical characteristics of the device. This transducer will find applications in many engineering fields for pressure measurement.

Lithium halide monolayers: Structural, electronic and optical properties by first principles study

NASA Astrophysics Data System (ADS)

Safari, Mandana; Maskaneh, Pegah; Moghadam, Atousa Dashti; Jalilian, Jaafar

2016-09-01

Using first principle study, we investigate the structural, electronic and optical properties of lithium halide monolayers (LiF, LiCl, LiBr). In contrast to graphene and other graphene-like structures that form hexagonal rings in plane, these compounds can form and stabilize in cubic shape interestingly. The type of band structure in these insulators is identified as indirect type and ionic nature of their bonds are illustrated as well. The optical properties demonstrate extremely transparent feature for them as a result of wide band gap in the visible range; also their electron transitions are indicated for achieving a better vision on the absorption mechanism in these kinds of monolayers.

Nonadiabatic one-electron transfer mechanism for the O-O bond formation in the oxygen-evolving complex of photosystem II

NASA Astrophysics Data System (ADS)

Shoji, Mitsuo; Isobe, Hiroshi; Shigeta, Yasuteru; Nakajima, Takahito; Yamaguchi, Kizashi

2018-04-01

The reaction mechanism of the O2 formation in the S4 state of the oxygen-evolving complex of photosystem II was clarified at the quantum mechanics/molecular mechanics (QM/MM) level. After the Yz (Y161) oxidation and the following proton transfer in the S3 state, five reaction steps are required to produce the molecular dioxygen. The highest barrier step is the first proton transfer reaction (0 → 1). The following reactions involving electron transfers were precisely analyzed in terms of their energies, structures and spin densities. We found that the one-electron transfer from the Mn4Ca cluster to Y161 triggers the O-O sigma bond formation.

Bonding in Heavier Group 14 Zero-Valent Complexes-A Combined Maximum Probability Domain and Valence Bond Theory Approach.

PubMed

Turek, Jan; Braïda, Benoît; De Proft, Frank

2017-10-17

The bonding in heavier Group 14 zero-valent complexes of a general formula L 2 E (E=Si-Pb; L=phosphine, N-heterocyclic and acyclic carbene, cyclic tetrylene and carbon monoxide) is probed by combining valence bond (VB) theory and maximum probability domain (MPD) approaches. All studied complexes are initially evaluated on the basis of the structural parameters and the shape of frontier orbitals revealing a bent structural motif and the presence of two lone pairs at the central E atom. For the VB calculations three resonance structures are suggested, representing the "ylidone", "ylidene" and "bent allene" structures, respectively. The influence of both ligands and central atoms on the bonding situation is clearly expressed in different weights of the resonance structures for the particular complexes. In general, the bonding in the studied E 0 compounds, the tetrylones, is best described as a resonating combination of "ylidone" and "ylidene" structures with a minor contribution of the "bent allene" structure. Moreover, the VB calculations allow for a straightforward assessment of the π-backbonding (E→L) stabilization energy. The validity of the suggested resonance model is further confirmed by the complementary MPD calculations focusing on the E lone pair region as well as the E-L bonding region. Likewise, the MPD method reveals a strong influence of the σ-donating and π-accepting properties of the ligand. In particular, either one single domain or two symmetrical domains are found in the lone pair region of the central atom, supporting the predominance of either the "ylidene" or "ylidone" structures having one or two lone pairs at the central atom, respectively. Furthermore, the calculated average populations in the lone pair MPDs correlate very well with the natural bond orbital (NBO) populations, and can be related to the average number of electrons that is backdonated to the ligands. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dissociative adsorption of a multifunctional compound on a semiconductor surface: a theoretical study of the adsorption of hydroxylamine on Ge(100).

PubMed

Park, Hyunkyung; Kim, Do Hwan

2018-06-06

The adsorption behavior of hydroxylamine on a Ge(100) surface was investigated using density functional theory (DFT) calculations. These calculations predicted that hydroxylamine, a multifunctional compound consisting of a hydroxyl group and an amine group, would initially become adsorbed through N-dative bonding, or alternatively through the hydroxyl group via O-H dissociative adsorption. An N-O dissociative reaction may also occur, mainly via N-dative molecular adsorption, and the N-O dissociative product was calculated to be the most stable of all the possible adsorption structures. The calculations furthermore indicated the formation of the N-O dissociative product from the N-dative structure to be nearly barrierless and the dissociated hydroxyl and amine groups to be bonded to two Ge atoms of adjacent Ge dimers. Simulated STM images suggested the change in electron density that would occur upon adsorption of hydroxylamine in various adsorption configurations, and specifically indicated the N-O dissociative product to have greater electron density around the amine groups, and the hydroxyl groups to mainly contribute electron density to the unoccupied electronic states.

TEM-EELS Investigation of Boron and Phosphorus Passivated 4H-SiC/SiO2 Interface Structures

NASA Astrophysics Data System (ADS)

Klingshirn, Christopher; Taillon, Joshua; Liu, Gang; Dhar, Sarit; Feldman, Leonard; Zheleva, Tsvetanka; Lelis, Aivars; Salamanca-Riba, Lourdes

A high density of electronic defects at the SiC/SiO2 interface adversely affects SiC-based metal oxide semiconductor devices. Various treatments are known to improve device performance. Annealing in a nitric oxide (NO) environment, for example, passivates electronic defects at the interface and raises the carrier mobility in the active region to 35-40 cm2/Vs, but the effect saturates after about 60 minutes of annealing. Passivation with phosphorus or boron improves upon NO by a factor of 2, increasing the mobility to over 90 cm2/Vs.2 We investigate the chemical and structural effects of these treatments on the SiC/SiO2 transition layer using high-resolution transmission electron microscopy (HRTEM) and high angle annular dark field (HAADF). Electron energy loss spectroscopy Spectrum Imaging (EELS SI) collected across the transition region allow identification of the width, composition and types of bonding at the transition layer. Advanced machine learning techniques applied to the EELS data reveal intermediate bonding states within this region. Supported by ARL under Grant No. W911NF1420110.

Simulation of charge transfer and orbital rehybridization in molecular and condensed matter systems

NASA Astrophysics Data System (ADS)

Nistor, Razvan A.

The mixing and shifting of electronic orbitals in molecules, or between atoms in bulk systems, is crucially important to the overall structure and physical properties of materials. Understanding and accurately modeling these orbital interactions is of both scientific and industrial relevance. Electronic orbitals can be perturbed in several ways. Doping, adding or removing electrons from systems, can change the bond-order and the physical properties of certain materials. Orbital rehybridization, driven by either thermal or pressure excitation, alters the short-range structure of materials and changes their long-range transport properties. Macroscopically, during bond formation, the shifting of electronic orbitals can be interpreted as a charge transfer phenomenon, as electron density may pile up around, and hence, alter the effective charge of, a given atom in the changing chemical environment. Several levels of theory exist to elucidate the mechanisms behind these orbital interactions. Electronic structure calculations solve the time-independent Schrodinger equation to high chemical accuracy, but are computationally expensive and limited to small system sizes and simulation times. Less fundamental atomistic calculations use simpler parameterized functional expressions called force-fields to model atomic interactions. Atomistic simulations can describe systems and time-scales larger and longer than electronic-structure methods, but at the cost of chemical accuracy. In this thesis, both first-principles and phenomenological methods are addressed in the study of several encompassing problems dealing with charge transfer and orbital rehybridization. Firstly, a new charge-equilibration method is developed that improves upon existing models to allow next-generation force-fields to describe the electrostatics of changing chemical environments. Secondly, electronic structure calculations are used to investigate the doping dependent energy landscapes of several high-temperature superconducting materials in order to parameterize the apparently large nonlinear electron-phonon coupling. Thirdly, ab initio simulations are used to investigate the role of pressure-driven structural re-organization in the crystalline-to-amorphous (or, metallic-to-insulating) transition of a common binary phase-change material composed of Ge and Sb. Practical applications of each topic will be discussed. Keywords. Charge-equilibration methods, molecular dynamics, electronic structure calculations, ab initio simulations, high-temperature superconductors, phase-change materials.

The nature of chemical bonding in actinide and lanthanide ferrocyanides determined by X-ray absorption spectroscopy and density functional theory.

PubMed

Dumas, Thomas; Guillaumont, Dominique; Fillaux, Clara; Scheinost, Andreas; Moisy, Philippe; Petit, Sébastien; Shuh, David K; Tyliszczak, Tolek; Den Auwer, Christophe

2016-01-28

The electronic properties of actinide cations are of fundamental interest to describe intramolecular interactions and chemical bonding in the context of nuclear waste reprocessing or direct storage. The 5f and 6d orbitals are the first partially or totally vacant states in these elements, and the nature of the actinide ligand bonds is related to their ability to overlap with ligand orbitals. Because of its chemical and orbital selectivities, X-ray absorption spectroscopy (XAS) is an effective probe of actinide species frontier orbitals and for understanding actinide cation reactivity toward chelating ligands. The soft X-ray probes of the light elements provide better resolution than actinide L3-edges to obtain electronic information from the ligand. Thus coupling simulations to experimental soft X-ray spectral measurements and complementary quantum chemical calculations yields quantitative information on chemical bonding. In this study, soft X-ray XAS at the K-edges of C and N, and the L2,3-edges of Fe was used to investigate the electronic structures of the well-known ferrocyanide complexes K4Fe(II)(CN)6, thorium hexacyanoferrate Th(IV)Fe(II)(CN)6, and neodymium hexacyanoferrate KNd(III)Fe(II)(CN)6. The soft X-ray spectra were simulated based on quantum chemical calculations. Our results highlight the orbital overlapping effects and atomic effective charges in the Fe(II)(CN)6 building block. In addition to providing a detailed description of the electronic structure of the ferrocyanide complex (K4Fe(II)(CN)6), the results strongly contribute to confirming the actinide 5f and 6d orbital oddity in comparison to lanthanide 4f and 5d.

The nature of chemical bonding in actinide and lanthanide ferrocyanides determined by X-ray absorption spectroscopy and density functional theory

DOE PAGES

Dumas, Thomas; Guillaumont, Dominique; Fillaux, Clara; ...

2016-01-01

The electronic properties of actinide cations are of fundamental interest to describe intramolecular interactions and chemical bonding in the context of nuclear waste reprocessing or direct storage. The 5f and 6d orbitals are the first partially or totally vacant states in these elements, and the nature of the actinide ligand bonds is related to their ability to overlap with ligand orbitals. Because of its chemical and orbital selectivities, X-ray absorption spectroscopy (XAS) is an effective probe of actinide species frontier orbitals and for understanding actinide cation reactivity toward chelating ligands. The soft X-ray probes of the light elements provide bettermore » resolution than actinide L 3 -edges to obtain electronic information from the ligand. Thus coupling simulations to experimental soft X-ray spectral measurements and complementary quantum chemical calculations yields quantitative information on chemical bonding. In this study, soft X-ray XAS at the K-edges of C and N, and the L 2,3 -edges of Fe was used to investigate the electronic structures of the well-known ferrocyanide complexes K 4 Fe II (CN) 6 , thorium hexacyanoferrate Th IV Fe II (CN) 6 , and neodymium hexacyanoferrate KNd III Fe II (CN) 6 . The soft X-ray spectra were simulated based on quantum chemical calculations. Our results highlight the orbital overlapping effects and atomic effective charges in the Fe II (CN) 6 building block. In addition to providing a detailed description of the electronic structure of the ferrocyanide complex (K 4 Fe II (CN) 6 ), the results strongly contribute to confirming the actinide 5f and 6d orbital oddity in comparison to lanthanide 4f and 5d.« less

Local bonding structure of tellurium and antimony in the phase change chalcogenides germanium-antimony-tellurium: A nuclear magnetic resonance study

NASA Astrophysics Data System (ADS)

Bobela, David C.

Recent technological applications of some chalcogenide materials, compounds containing a group VI atom, have prompted studies of the local atomic structure of the amorphous phase. In the case of Ge2Sb2Te 5, metastability in the local bonding structure is responsible for its usefulness as a phase-change memory material. There is no consensus on the exact phase-change mechanism, which is partly due to the inadequacy of standard scattering techniques to probe the structure of the amorphous phase. Nuclear magnetic resonance methods, on the other hand, are well suited to study local structural order even in the absence of a periodic lattice. In this technique, structural information is encoded as an oscillating voltage caused by the nuclear spin. For the tellurium isotope, 125Te (spin = 1/2 in the ground state), the dominant interaction comes from the core and valence electrons that carry angular momentum. This interaction is helpful in identifying Te sites of different local coordination since the number of neighboring atoms should markedly change the local electronic structure. The antimony isotope 125Sb has a spin = 5/2 in the ground state and possesses an asymmetric nuclear charge. This quadrupole moment will interact with an electric field gradient at the nuclear site, which is provided by an asymmetric electron cloud surrounding the nucleus. The frequency-space spectra will reflect the strength of the interaction as well as the symmetry of the local electronic environment. This work investigates the nuclear magnetic resonance spectrum of 125Te and 125Sb in the crystalline and amorphous forms of several GexSbyTe 1-x-y compounds where 0 < (x, y) < 1. Results from the crystalline phase 125Te data show a trend in the spectral position that can be related to the tellurium bonded to three and six neighbors. In the amorphous phase, the same trend is observed, and the nuclear magnetic resonance fingerprint of two-fold and three-fold coordinated tellurium is obtained. It is concluded, based upon this comparison that the Te atoms see a dramatically different bonding environment depending on which phase the lattice has. The 125Sb data for the crystalline phase indicate electric field gradients that are consistent with similarly bonded quadrupolar nuclei, such as Sb atoms in crystalline Sb or five-fold coordinated Sb in crystalline MnSb. The NMR data exemplify the consequences of combinatorial disorder on the spectra via the absence of certain line-shape features. In the amorphous phase, the electric field gradients are approximately seven times larger, and the fingerprints of both highly-symmetric and asymmetric antimony sites emerge. Details of field gradient, i.e. the magnitude and symmetry, are remarkably similar to those found in Sb containing compounds where the Sb sites are three-fold pyramidal, such as in crystalline Sb2X3 where X = O, S, or Se. The observations from the NMR data provide a critical litmus test for recent structural models of the amorphous phase. In particular, the amorphous phase data provides clear evidence that the Te atoms are two-fold and three-fold coordinated while the Sb atoms are most likely bonded in three-fold pyramidal configurations. These observations imply a structural model of the amorphous phase that agrees best with a models based upon the "8 minus n", or "8-n" rule for chemical bonding in amorphous semiconductors. Thus, the lattice of these compounds is arranged such that the constituent elements have enough bonds, on average, to satisfy their valence requirement. The implications of the NMR data on theoretical modeling data are immediate. Theoretical models of these systems must possess some aspect of the "8-n" mentality. With this idea as a foundation for physically realistic representations of the amorphous phase, the origin of the phase-change mechanism may be unraveled, which will ultimately speed the process of compositional optimization of phase-change materials.

Chemical and Physical Approaches to the Modulation of the Electronic Structure, Conductivities and Optical Properties of SWNT Thin Films

NASA Astrophysics Data System (ADS)

Moser, Matthew Lee

Since their discovery two decades ago, single walled carbon nanotubes (SWNT) have created an expansion of scientific interest that continues to grow to this day. This is due to a good balance between presence of bandgap, chemical reactivity and electrical conductivity. By interconnection of the individual nanotubes or modulation of the SWNT's electronic states, electronic devices made with thin films can become candidates for next generation electronics in areas such as memory devices, spintronics, energy storage devices and optoelectronics. My thesis focuses on the modulation of the electronic structure, optical properties and transport characteristics of single walled carbon nanotube films and their application in electronic and optoelectronic devices. Individual SWNTs have exceptional electronic properties but are difficult to manipulate for use in electronic devices. Alternatively, devices utilize SWNTs in thin films. SWNT thin films, however, may lose some of the properties due to Schottky barriers and electron hoping between metal-nanotube junctions and individual nanotubes within the film, respectively. Until recently, there has been no known route to preserve both conjugation and electrical properties. Prior attempts using covalent chemical functionalization led to re-hybridization of sp2 carbon centers to sp3, which introduces defects into the material and results in a decrease of electron mobility. As was discovered in Haddon Research group, depositing Group VI transition metals via atomic vapor deposition into SWNT films results in formation of bis-hexahapto covalent bonds. This (eta6-SWNT) Metal (eta6-SWNT) type of bonding was found to interconnect the delocalized systems without inducing structural re-hybridization and results in a decrease of the thin films electrical resistance. Recently, with the assistance of electron beam deposition, we deposited atomic metal vapor of various lanthanide metals on the SWNT thin films with the idea that they would also form covalent interconnects between nanotube sidewalls. In the case of highly electropositive lanthanides, the possibility of hexahapto bonding combined with ionic character can be evaluated and theorized. We have reported the first use of lanthanides to enhance the conductivities of SWNT thin films and showed that these metals can not only form bis-hexahapto interconnects at the SWNT junctions but can also inject electrons into the conduction bands of the SWNTs, forming a new type of mixed covalent-ionic bonding in the SWNT network. By monitoring electrical resistance and taking spectroscopic measurements of the Near-Infrared region we are able to show the correlation between enhanced conductivity and suppression of the S 11 interband transition of semiconducting SWNTs. Potential applications of SWNT thin films as electrochromic windows require reversible modulation of the electronic structure. In order to fabricate SWNTs devices which allow for this behavior it is necessary to modulate the electronic structure by physical means such as the application of an electrical potential. We found that ionic solutions can assist with maintaining complete suppression of two Van Hove singularities in the Density of States of semiconducting SWNTs which results in optically transparent windows in the Near-Infrared region, similar to the effect seen with the incorporation of atomic lanthanide metals in thin films. We demonstrate this behavior to provide a route to nanotube based optoelectronic devices in which we use electric fields to reversibly dope the SWNT films and thereby achieve controllable modulation of optical properties of SWNT thin film.

Role of Hydrogen Bonding in Photoinduced Electron-Proton Transfer from Phenols to a Polypyridine Ru Complex with a Proton-Accepting Ligand

DOE PAGES

Lymar, Sergei V.; Ertem, Mehmed Z.; Lewandowska-Andralojc, Anna; ...

2017-08-09

Electron-proton transfer, EPT, from phenols to a triplet MLCT-excited Ru polypyridine complex containing an uncoordinated nitrogen site, 1(T), can be described by a kinetic model that accounts for the H-bonding of 1(T) to phenol, 1(T) to solvent, and phenol to solvent. The latter plays a major role in the kinetic solvent effect and commonly precludes simultaneous determination of the EPT rate constant and 1(T)-phenol H-bonding constant. A number of these quantities previously reported for similar systems are shown to be in error due to an inconsistent data analysis. In conclusion, control experiments replacing either 1(T) by its structural isomer withmore » a sterically screened nitrogen site or phenol by its H-bonding surrogate, trifluoroethanol, and the observation of negative activation enthalpies for the overall reactions between 1(T) and phenols lend support to the proposed model and provide evidence for the formation of a precursor H-bonded complex between the reactants, which is a prerequisite for EPT.« less

Hydrogen bonding in water clusters and their ionized counterparts.

PubMed

Neela, Y Indra; Mahadevi, A Subha; Sastry, G Narahari

2010-12-30

Ab initio and DFT computations were carried out on four distinct hydrogen-bonded arrangements of water clusters (H(2)O)(n), n = 2-20, represented as W1D, W2D, W2DH, and W3D. The variation in the strength of hydrogen bond as a function of the chain length is studied. In all the four cases, there is a substantial cooperative interaction, albeit in different degrees. The effect of basis set superposition error (BSSE) on the complexation energy of water clusters has been analyzed. Atoms in molecules (AIM) analysis performed to evaluate the nature of the hydrogen bonding shows a high correlation between hydrogen bond strength and the trends in complexation energy. Solvated water clusters exhibit lower complexation energies compared to corresponding gas-phase geometries on PCM (polarized continuum model) optimization. The feasibility of stripping an electron or addition of an electron increases dramatically as the cluster size increases. Although W3D caged structures are stable for neutral clusters, the helical W2DH arrangement appeared to be an optimal choice for its ionized counterparts.

Role of Hydrogen Bonding in Photoinduced Electron-Proton Transfer from Phenols to a Polypyridine Ru Complex with a Proton-Accepting Ligand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lymar, Sergei V.; Ertem, Mehmed Z.; Lewandowska-Andralojc, Anna

Electron-proton transfer, EPT, from phenols to a triplet MLCT-excited Ru polypyridine complex containing an uncoordinated nitrogen site, 1(T), can be described by a kinetic model that accounts for the H-bonding of 1(T) to phenol, 1(T) to solvent, and phenol to solvent. The latter plays a major role in the kinetic solvent effect and commonly precludes simultaneous determination of the EPT rate constant and 1(T)-phenol H-bonding constant. A number of these quantities previously reported for similar systems are shown to be in error due to an inconsistent data analysis. In conclusion, control experiments replacing either 1(T) by its structural isomer withmore » a sterically screened nitrogen site or phenol by its H-bonding surrogate, trifluoroethanol, and the observation of negative activation enthalpies for the overall reactions between 1(T) and phenols lend support to the proposed model and provide evidence for the formation of a precursor H-bonded complex between the reactants, which is a prerequisite for EPT.« less

Formation and Characterization of Silver Nanoparticle Composite with Poly(p-Br/F-phenylsilane).

PubMed

Roh, Sung-Hee; Noh, Ji Eun; Woo, Hee-Gweon; Cho, Myong-Shik; Sohn, Honglae

2015-02-01

The one-pot production and structural characterization of composites of silver nanoparticles with poly(p-Br/F-phenylsilane), Br/F-PPS, have been performed. The conversion of Ag+ ions to stable Ag0 nanoparticles is mediated by the copolymer Br/F-PPS having both possibly reactive Si-H bonds in the polymer backbone and C-Br bonds in the substituents along with relatively inert C-F bonds. Transmission electron microscopy and field emission scanning electron microscopy analyses show the formation of the composites where silver nanoparticles (less than 30 nm of size) are well dispersed over the Br/F-PPS matrix. X-ray diffraction patterns are consistent with that for face-centered-cubic typed silver. The polymer solubility in toluene implys that the cleavage of C-Br bond and the Si-F dative bonding may not be occurred appreciably at ambient temperature. Nonetheless, thermogravimetric analysis data suggest that some sort of cross-linking could take place at high temperature. Most of the silver particles undergo macroscopic aggregation without Br/F-PPS, which indicates that the polysilane is necessary for stabilizing the silver nanoparticles.

Structural properties of thiophenes investigated with simulations of a coarse-grained model

NASA Astrophysics Data System (ADS)

Luettmer-Strathmann, Jutta; Almutairi, Amani

Thiophenes have important applications in organic electronics, energy conversion, and storage. The interfacial layer of an organic semiconductor in contact with a metal electrode has important effects on the performance of thin-film devices. However, the structure of this layer is not easy to model. In recent work, we developed a coarse-grained model for alpha-oligothiophenes in the bulk and near gold surfaces. We describe the molecules as linear chains of bonded, discotic particles with Gay-Berne potential interactions between non-bonded ellipsoids. In this work, we investigate structural properties of thiophenes with simulations of our coarse-grained model.

Origins of the structural phase transitions in MoTe2 and WTe2

NASA Astrophysics Data System (ADS)

Kim, Hyun-Jung; Kang, Seoung-Hun; Hamada, Ikutaro; Son, Young-Woo

2017-05-01

Layered transition metal dichalcogenides MoTe2 and WTe2 share almost similar lattice constants as well as topological electronic properties except their structural phase transitions. While the former shows a first-order phase transition between monoclinic and orthorhombic structures, the latter does not. Using a recently proposed van der Waals density functional method, we investigate structural stability of the two materials and uncover that the disparate phase transitions originate from delicate differences between their interlayer bonding states near the Fermi energy. By exploiting the relation between the structural phase transitions and the low energy electronic properties, we show that a charge doping can control the transition substantially, thereby suggesting a way to stabilize or to eliminate their topological electronic energy bands.

On the dynamical nature of the active center in a single-site photocatalyst visualized by 4D ultrafast electron microscopy

PubMed Central

Yoo, Byung-Kuk; Su, Zixue; Thomas, John Meurig; Zewail, Ahmed H.

2016-01-01

Understanding the dynamical nature of the catalytic active site embedded in complex systems at the atomic level is critical to developing efficient photocatalytic materials. Here, we report, using 4D ultrafast electron microscopy, the spatiotemporal behaviors of titanium and oxygen in a titanosilicate catalytic material. The observed changes in Bragg diffraction intensity with time at the specific lattice planes, and with a tilted geometry, provide the relaxation pathway: the Ti4+=O2− double bond transformation to a Ti3+−O1− single bond via the individual atomic displacements of the titanium and the apical oxygen. The dilation of the double bond is up to 0.8 Å and occurs on the femtosecond time scale. These findings suggest the direct catalytic involvement of the Ti3+−O1− local structure, the significance of nonthermal processes at the reactive site, and the efficient photo-induced electron transfer that plays a pivotal role in many photocatalytic reactions. PMID:26729878

Lewis acid-base interactions in weakly bound formaldehyde complexes with CO2, HCN, and FCN: considerations on the cooperative H-bonding effects.

PubMed

Rivelino, Roberto

2008-01-17

Ab initio quantum chemistry calculations reveal that HCN and mainly FCN can form Lewis acid-base complexes with formaldehyde associated with cooperative H bonds, as first noticed by Wallen et al. (Blatchford, M. A.; Raveendran, P.; Wallen, S. L. J. Am. Chem. Soc. 2002, 124, 14818-14819) for CO2-philic materials under supercritical conditions. The present results, obtained with MP2(Full)/aug-cc-pVDZ calculations, show that the degeneracy of the nu(2) mode in free HCN or FCN is removed upon complexation in the same fashion as that of CO2. The splitting of these bands along with the electron structure analysis provides substantial evidence of the interaction of electron lone pairs of the carbonyl oxygen with the electron-deficient carbon atom of the cyanides. Also, this work investigates the role of H bonds acting as additional stabilizing interactions in the complexes by performing the energetic and geometric characterization.

2-Amino-3-methyl-6-[meth­yl­(phen­yl)­amino]-5-nitro­pyrimidin-4(3H)-one: polarized mol­ecules within hydrogen-bonded sheets

PubMed Central

Rodríguez, Ricaurte; Nogueras, Manuel; Cobo, Justo; Glidewell, Christopher

2009-01-01

The pyrimidinone ring in the title compound, C12H13N5O3, is effectively planar, despite the presence of five substituents. The bond distances provide evidence for significant polarization of the electronic structure, with charge separation, and the mol­ecules are linked into sheets by a combination of N—H⋯O and N—H⋯π(arene) hydrogen bonds. Comparisons are made with the mol­ecular and supra­molecular structures of the precursor compound 2-amino-6-[meth­yl(phen­yl)amino]-5-nitro­pyrimidin-4(3H)-one. PMID:19726857

Computational study of the electronic structure and magnetic properties of the Ni-C state in [NiFe] hydrogenases including the second coordination sphere.

PubMed

Kampa, Mario; Lubitz, Wolfgang; van Gastel, Maurice; Neese, Frank

2012-12-01

[NiFe] hydrogenases catalyze the reversible formation of H(2). The [NiFe] heterobimetallic active site is rich in redox states. Here, we investigate the key catalytic state Ni-C of Desulfovibrio vulgaris Miyazaki F hydrogenase using a cluster model that includes the truncated amino acids of the entire second coordination sphere of the enzyme. The optimized geometries, computed g tensors, hyperfine coupling constants, and IR stretching frequencies all agree well with experimental values. For the hydride in the bridging position, only a single minimum on the potential energy surface is found, indicating that the hydride bridges and binds to both nickel and iron. The influence of the second coordination sphere on the electronic structure is investigated by comparing results from the large cluster models with truncated models. The largest interactions of the second coordination sphere with the active site concern the hydrogen bonds with the cyanide ligands, which modulate the bond between iron and these ligands. Secondly, the electronic structure of the active site is found to be sensitive to the protonation state of His88. This residue forms a hydrogen bond with the spin-carrying sulfur atom of Cys549, which in turn tunes the spin density at the nickel and coordinating sulfur atoms. In addition, the unequal distribution of spin density over the equatorial cysteine residues results from different orientations of the cysteine side chains, which are kept in their particular orientation by the secondary structure of the protein.

Electronic structure of Ag7GeS5I superionic compound

NASA Astrophysics Data System (ADS)

Bletskan, Dmytro; Studenyak, Ihor; Bletskan, Mykhailo; Vakulchak, Vasyl

2018-05-01

This paper presents the originally results of ab initio calculations of electronic structure, total and partial densities of electronic states as well as electronic charge density distribution of Ag7GeS5I crystal performed within the density functional theory (DFT) in the local density approximation (LDA) for exchange-correlation potential. According to performed calculations, Ag7GeS5I is the direct-gap semiconductor with the valence band top and the conductivity band bottom in the Γ point of Brillouin zone. The band gap width calculated in the LDA-approximation is Egd = 0.73 eV. The analysis of total and partial densities of electronic states allow us to identify the atomic orbital contributions into the crystal orbitals as well as the formation data of chemical bond in the studied crystal. In the top part of Ag7GeS5I valence band it was revealed the considerable mixing (hybridization) of the occupied d-states of Ag noble metal and the delocalized p-states of sulfur and iodine, which is undoubtedly associated with the covalent character of chemical bond between S, I atoms and noble metal atom.

Multinuclear Solid-State Magnetic Resonance as a Sensitive Probe of Structural Changes upon the Occurrence of Halogen Bonding in Co-crystals.

PubMed

Widdifield, Cory M; Cavallo, Gabriella; Facey, Glenn A; Pilati, Tullio; Lin, Jingxiang; Metrangolo, Pierangelo; Resnati, Giuseppe; Bryce, David L

2013-09-02

Although the understanding of intermolecular interactions, such as hydrogen bonding, is relatively well-developed, many additional weak interactions work both in tandem and competitively to stabilize a given crystal structure. Due to a wide array of potential applications, a substantial effort has been invested in understanding the halogen bond. Here, we explore the utility of multinuclear ((13)C, (14/15)N, (19)F, and (127)I) solid-state magnetic resonance experiments in characterizing the electronic and structural changes which take place upon the formation of five halogen-bonded co-crystalline product materials. Single-crystal X-ray diffraction (XRD) structures of three novel co-crystals which exhibit a 1:1 stoichiometry between decamethonium diiodide (i.e., [(CH3)3N(+)(CH2)10N(+)(CH3)3][2 I(-)]) and different para-dihalogen-substituted benzene moieties (i.e., p-C6X2Y4, X=Br, I; Y=H, F) are presented. (13)C and (15)N NMR experiments carried out on these and related systems validate sample purity, but also serve as indirect probes of the formation of a halogen bond in the co-crystal complexes in the solid state. Long-range changes in the electronic environment, which manifest through changes in the electric field gradient (EFG) tensor, are quantitatively measured using (14)N NMR spectroscopy, with a systematic decrease in the (14)N quadrupolar coupling constant (CQ) observed upon halogen bond formation. Attempts at (127)I solid-state NMR spectroscopy experiments are presented and variable-temperature (19)F NMR experiments are used to distinguish between dynamic and static disorder in selected product materials, which could not be conclusively established using solely XRD. Quantum chemical calculations using the gauge-including projector augmented-wave (GIPAW) or relativistic zeroth-order regular approximation (ZORA) density functional theory (DFT) approaches complement the experimental NMR measurements and provide theoretical corroboration for the changes in NMR parameters observed upon the formation of a halogen bond. Copyright © 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

UV Photofragmentation Dynamics of Protonated Cystine: Disulfide Bond Rupture.

PubMed

Soorkia, Satchin; Dehon, Christophe; Kumar, S Sunil; Pedrazzani, Mélanie; Frantzen, Emilie; Lucas, Bruno; Barat, Michel; Fayeton, Jacqueline A; Jouvet, Christophe

2014-04-03

Disulfide bonds (S-S) play a central role in stabilizing the native structure of proteins against denaturation. Experimentally, identification of these linkages in peptide and protein structure characterization remains challenging. UV photodissociation (UVPD) can be a valuable tool in identifying disulfide linkages. Here, the S-S bond acts as a UV chromophore and absorption of one UV photon corresponds to a σ-σ* transition. We have investigated the photodissociation dynamics of protonated cystine, which is a dimer of two cysteines linked by a disulfide bridge, at 263 nm (4.7 eV) using a multicoincidence technique in which fragments coming from the same fragmentation event are detected. Two types of bond cleavages are observed corresponding to the disulfide (S-S) and adjacent C-S bond ruptures. We show that the S-S cleavage leads to three different fragment ions via three different fragmentation mechanisms. The UVPD results are compared to collision-induced dissociation (CID) and electron-induced dissociation (EID) studies.

A computational study of dimers and trimers of nitrosyl hydride: Blue shift of NH bonds that are involved in H-bond and orthogonal interactions

NASA Astrophysics Data System (ADS)

Solimannejad, Mohammad; Massahi, Shokofeh; Alkorta, Ibon

2009-07-01

Ab initio calculations at MP2/aug-cc-pVTZ level were used to analyze the interactions between nitrosyl hydride (HNO) dimers and trimers. The structures obtained have been analyzed with the Atoms in Molecules (AIMs) and Natural Bond Orbital (NBO) methodologies. Four minima were located on the potential energy surface of the dimers. Nine different structures have been obtained for the trimers. Three types of interactions are observed, NH⋯N and NH⋯O hydrogen bonds and orthogonal interaction between the lone pair of the oxygen with the electron-deficient region of the nitrogen atom. Stabilization energies of dimers and trimers including BSSE and ZPE are in the range 4-8 kJ mol -1 and 12-19 kJ mol -1, respectively. Blue shift of NH bond upon complex formation in the ranges between 30-80 and 14,114 cm -1 is predicted for dimers and trimers, respectively.

Characterizing bonding patterns in diradicals and triradicals by density-based wave function analysis: A uniform approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orms, Natalie; Rehn, Dirk; Dreuw, Andreas

Density-based wave function analysis enables unambiguous comparisons of electronic structure computed by different methods and removes ambiguity of orbital choices. Here, we use this tool to investigate the performance of different spin-flip methods for several prototypical diradicals and triradicals. In contrast to previous calibration studies that focused on energy gaps between high and low spin-states, we focus on the properties of the underlying wave functions, such as the number of effectively unpaired electrons. Comparison of different density functional and wave function theory results provides insight into the performance of the different methods when applied to strongly correlated systems such asmore » polyradicals. We also show that canonical molecular orbitals for species like large copper-containing diradicals fail to correctly represent the underlying electronic structure due to highly non-Koopmans character, while density-based analysis of the same wave function delivers a clear picture of bonding pattern.« less

Computational insight into the reaction intermediates in the glycosylation reaction assisted by donor heteroatoms.

PubMed

Bravo, Fernando; Viso, Antonio; Alcázar, Eva; Molas, Pineda; Bo, Carles; Castillón, Sergio

2003-02-07

We studied the geometric and electronic structure of several cations (9 and 18-23) that are usually proposed as intermediates for glycosylation reactions using DFT methods. For ions 9 and 18-23 the geometries obtained corresponded to an open ion (6b type) irrespective of the exocyclic heteroatom (S, Se, I) and the size of the cycle (furanoses as well as pyranoses). We studied how substituents bonded to the exocyclic heteroatom (R in SR and SeR) affect the structure of ions and found that the geometry approached that of episulfonium and episelenonium ions (6a type) when the substituents were electron donors. The tert-butyl group and the 2,4,6-trimethyl- and 2,4,6-trimethoxyphenyl and trimethylsilyl groups produced the strongest of these effects. The presence of an electron-withdrawing group (CO-CF(3)) bonded to the hydroxymethyl group produced a similar but weaker effect. We analyzed this behavior in terms of molecular orbital interactions.

Characterizing bonding patterns in diradicals and triradicals by density-based wave function analysis: A uniform approach

DOE PAGES

Orms, Natalie; Rehn, Dirk; Dreuw, Andreas; ...

2017-12-21

Density-based wave function analysis enables unambiguous comparisons of electronic structure computed by different methods and removes ambiguity of orbital choices. Here, we use this tool to investigate the performance of different spin-flip methods for several prototypical diradicals and triradicals. In contrast to previous calibration studies that focused on energy gaps between high and low spin-states, we focus on the properties of the underlying wave functions, such as the number of effectively unpaired electrons. Comparison of different density functional and wave function theory results provides insight into the performance of the different methods when applied to strongly correlated systems such asmore » polyradicals. We also show that canonical molecular orbitals for species like large copper-containing diradicals fail to correctly represent the underlying electronic structure due to highly non-Koopmans character, while density-based analysis of the same wave function delivers a clear picture of bonding pattern.« less

Chemical scissors cut phosphorene and their novel electronic properties

NASA Astrophysics Data System (ADS)

Peng, Xihong; Wei, Qun

2015-03-01

Phosphorene, a recently fabricated two-dimensional puckered honeycomb structure of black phosphorus, showed promising properties for applications in nano-electronics. In this work, we report a chemical scissors effect on phosphorene, using first principles density-functional methods. It was found that chemical species, such as H, OH, F, and Cl, can act as scissors to cut phosphorene. Phosphorus nanochains and nanoribbons can be obtained using such chemical scissors. The scissors effect results from the strong bonding between the chemical species and phosphorus atoms. Other species such as O, S and Se fail to cut phosphorene due to their weak bonding with phosphorus. The electronic structures of the produced P-chains reveal that the hydrogenated P-chain is an insulator; however, the pristine P-chain is a one-dimensional Dirac material, in which the charge carriers are massless fermions travelling at an effective speed of light approximately 8x105 m/s. The obtained zigzag phosphorene nanoribbons show either metallic or semiconducting behaviors, depending on the treatment of the edge phosphorus atoms.

Interlaced crystals having a perfect Bravais lattice and complex chemical order revealed by real-space crystallography

DOE PAGES

Shen, Xiao; Hernandez-Pagan, Emil; Zhou, Wu; ...

2014-11-14

The search for optimal thermoelectric materials aims for structures in which the crystalline order is disrupted to lower the thermal conductivity without degradation of the electron conductivity. Here we report the synthesis and characterization of ternary nanoparticles (two cations and one anion) that exhibit a new form of crystal-line order: an uninterrupted, perfect, global Bravais lattice, in which the two cations exhibit a wide array of distinct ordering patterns within the cation sublattice, form-ing interlaced domains and phases. Partitioning into domains and phases is not unique; the corresponding boundaries have no structural defects or strain and entail no energy cost.more » We call this form of crystalline order “interlaced crystals” and present the example of hexagonal-CuInS 2. Interlacing is possible in multi-cation tetrahedral-ly-bonded compound with an average of two electrons per bond. Interlacing has min-imal effect on electronic properties, but should strongly reduce phonon transport, making interlaced crystals attractive for thermoelectric applications.« less

Spectroscopic, quantum chemical calculation and molecular docking of dipfluzine

NASA Astrophysics Data System (ADS)

Srivastava, Karnica; Srivastava, Anubha; Tandon, Poonam; Sinha, Kirti; Wang, Jing

2016-12-01

Molecular structure and vibrational analysis of dipfluzine (C27H29FN2O) were presented using FT-IR and FT-Raman spectroscopy and quantum chemical calculations. The theoretical ground state geometry and electronic structure of dipfluzine are optimized by the DFT/B3LYP/6-311++G (d,p) method and compared with those of the crystal data. The 1D potential energy scan was performed by varying the dihedral angle using B3LYP functional at 6-31G(d,p) level of theory and thus the most stable conformer of the compound were determined. Molecular electrostatic potential surface (MEPS), frontier orbital analysis and electronic reactivity descriptor were used to predict the chemical reactivity of molecule. Energies of intra- and inter-molecular hydrogen bonds in molecule and their electronic aspects were investigated by natural bond orbital (NBO). To find out the anti-apoptotic activity of the title compound molecular docking studies have been performed against protein Fas.

Dimers of nineteen-electron sandwich compounds: crystal and electronic structures, and comparison of reducing strengths.

PubMed

Mohapatra, Swagat K; Fonari, Alexandr; Risko, Chad; Yesudas, Kada; Moudgil, Karttikay; Delcamp, Jared H; Timofeeva, Tatiana V; Brédas, Jean-Luc; Marder, Seth R; Barlow, Stephen

2014-11-17

The dimers of some Group 8 metal cyclopentadienyl/arene complexes and Group 9 metallocenes can be handled in air, yet are strongly reducing, making them useful n-dopants in organic electronics. In this work, the X-ray molecular structures are shown to resemble those of Group 8 metal cyclopentadienyl/pentadienyl or Group 9 metal cyclopentadienyl/diene model compounds. Compared to those of the model compounds, the DFT HOMOs of the dimers are significantly destabilized by interactions between the metal and the central CC σ-bonding orbital, accounting for the facile oxidation of the dimers. The lengths of these CC bonds (X-ray or DFT) do not correlate with DFT dissociation energies, the latter depending strongly on the monomer stabilities. Ru and Ir monomers are more reducing than their Fe and Rh analogues, but the corresponding dimers also exhibit much higher dissociation energies, so the estimated monomer cation/neutral dimer potentials are, with the exception of that of [RhCp2 ]2 , rather similar (-1.97 to -2.15 V vs. FeCp2 (+/0) in THF). The consequences of the variations in bond strength and redox potentials for the reactivity of the dimers are discussed. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Design of the magnetic homonuclear bonds boron nitride nanosheets using DFT methods.

PubMed

Anota, E Chigo; Hernández, A Bautista; Morales, A Escobedo; Castro, M

2017-06-01

Design and characterization of the structural, electronic, and magnetic properties of armchair boron-nitride, BN (B 27 N 27 H 18 ), nanosheets were performed by means of density functional theory all-electron calculations. The HSEh1PBE-GGA method together with 6-31G(d) basis sets were used. Non-stoichiometric B 30 N 24 H 18 and B 24 N 30 H 18 compositions: rich in boron or nitrogen atoms, forming homonuclear B or N bonds, respectively, were chosen. The obtained results reveal that these BN nanosheets reach structural stability in the anionic form, where semiconductor and magnetic behaviors are promoted. Effectively, the HOMO-LUMO gap is of 2.03 and 2.39eV, respectively and the magnetic moments are of 1.0 magneton bohrs, coming from the boron atoms in both systems. The rich in boron nanosheets present high-polarity, either in the gas phase or embedded in aqueous mediums like water, as well as low chemical reactivity, signifying potential applicability in the transportation of pharmaceutical species in biological mediums. These systems are also promising for the design of electronic devices, because they possess low-work functions, mainly arising from the homonuclear boron or nitrogen bond formation. Copyright © 2017 Elsevier Inc. All rights reserved.

Cyclo-biphenalenyl biradicaloid molecular materials: conformation, tautomerization, magnetism, and thermochromism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Jingsong; Sumpter, Bobby G; Meunier, Vincent

2011-01-01

Phenalenyl and its derivatives have recently attracted a great deal of interest as a result of a 2-electron multicenter (2e/mc) covalent pi-pi bonding between two pi-stacked phenalenyl units. The 2e/mc bonded pi-dimers are close in energy to the sigma-dimers of phenalenyl and therefore fickle properties may emerge from bond fluctuation, yielding smart pi-functional materials. Here we examine the valence tautomerization of two cyclo-biphenalenyl biradicaloid molecular materials with chair- and boat-conformations by spin-restricted (R) and unrestricted (U) DFT using the M06 and B3LYP functionals. We found that the chair-conformation involves a 2e/4c pi-pi bonded structure while the boat-conformation involves a 2e/12cmore » pi-pi bonded structure on their potential energy surfaces. The global minimum for the chair-conformation is the sigma-bonded structure while it is the pi-pi bonded structure for the boat-conformation. The chair-conformation exhibits a stepwise [3,3]-sigmatropic rearrangement, and calculations predict a negligible paramagnetic susceptibility near room temperature. In comparison, the paramagnetism of the boat-conformation should be observable by SQUID and/or ESR. According to the difference of the global minima of the two conformations and the parameterized UV-Vis calculations, the color of the chair-conformation is expected to become darker while that of the boat-conformation become lighter with increasing temperature.« less

A theoretical investigation of the structural and electronic properties of 55-atom nanoclusters: The examples of Y–Tc and Pt

DOE Office of Scientific and Technical Information (OSTI.GOV)

Batista, Krys E. A.; Piotrowski, Maurício J., E-mail: mauriciomjp@gmail.com; Chaves, Anderson S.

2016-02-07

Several studies have found that the Pt{sub 55} nanocluster adopts a distorted reduced core structure, DRC{sub 55}, in which there are 8–11 atoms in the core and 47–44 atoms in the surface, instead of the compact and high-symmetry icosahedron structure, ICO{sub 55}, with 13 and 42 atoms in the core and surface, respectively. The DRC structure has also been obtained as the putative global minimum configuration (GMC) for the Zn{sub 55} (3d), Cd{sub 55} (4d), and Au{sub 55} (5d) systems. Thus, the DRC{sub 55} structure has been reported only for systems with a large occupation of the d-states, where themore » effects of the occupation of the valence anti-bonding d-states might play an important role. Can we observe the DRC structure for 55-atom transition-metal systems with non-occupation of the anti-bonding d-states? To address this question, we performed a theoretical investigation of the Y {sub 55}, Zr{sub 55}, Nb{sub 55}, Mo{sub 55}, Tc{sub 55}, and Pt{sub 55} nanoclusters, employing density functional theory calculations. For the putative GMCs, we found that the Y {sub 55} adopts the ICO{sub 55} structure, while Nb{sub 55} and Mo{sub 55} adopt a bulk-like fragment based on the hexagonal close-packed structure and Tc{sub 55} adopts a face-centered cubic fragment; however, Zr{sub 55} adopts a DRC{sub 55} structure, like Zn{sub 55}, Cd{sub 55}, Pt{sub 55}, and Au{sub 55}. Thus we can conclude that the preference for DRC{sub 55} structure is not related to the occupation of the anti-bonding d-states, but to a different effect, in fact, a combination of structural and electronic effects. Furthermore, we obtained that the binding energy per atom follows the occupation of the bonding and anti-bonding model, i.e., the stability of the studied systems increases from Y to Tc with a small oscillation for Mo, which also explains the equilibrium bond lengths. We obtained a larger magnetic moment for Y {sub 55} (31 μ{sub B}) which can be explained by the localization of the d-states in Y at nanoscale, which is not observed for the remaining systems (0–1 μ{sub B})« less

Impact of proton transfer phenomena on the electronic structure of model Schiff bases: an AIM/NBO/ELF study.

PubMed

Panek, Jarosław J; Filarowski, Aleksander; Jezierska-Mazzarello, Aneta

2013-10-21

Understanding of the electronic structure evolution due to a proton dynamics is a key issue in biochemistry and material science. This paper reports on density functional theory calculations of Schiff bases containing short, strong intramolecular hydrogen bonds where the bridged proton is located: (i) at the donor site, (ii) strongly delocalized, and (iii) at the acceptor site. The mobility of the bridged proton and its influence on the molecular structure and properties of the chosen Schiff base derivatives have been investigated on the basis of Atoms in Molecules, Natural Bond Orbitals, and Electron Localization Function theories. It has been observed that the extent of the bridged proton delocalization is strongly modified by the steric and inductive effects present in the studied compounds introduced by various substituents. It has been shown that: (i) potential energy profiles for the proton motion are extremely dependent on the substitution of the aromatic ring, (ii) the topology of the free electron pairs present at the donor∕acceptor site, as well as their electron populations, are affected qualitatively by the bridged proton position, (iii) the distortion of the molecular structure due to the bridged proton dynamics includes the atomic charge fluctuations, which are in some cases non-monotonic, and (iv) topology of the ELF recognizes events of proton detachment from the donor and attachment to the acceptor. The quantitative and qualitative results shed light onto molecular consequences of the proton transfer phenomena.

Small Water Cluster Cations

NASA Astrophysics Data System (ADS)

Novakovskaya, Yu. V.; Stepanov, N. F.

Structures of water cluster cations (H_{2}O)^{+}_{n} with n ≤ 5 are optimized at the unrestricted Hartree-Fock level with the 4 - 31 + +G** basis set. Energetic characteristics of the cations are then estimated taking into account the second order perturbation corrections (MP2). After the electron detachment from a neutral cluster, the structure of the latter substantially changes, so that OH and H3O+ fragments can be distinguished in it. In some cations H3O+ is so strongly bonded to water molecules that it is reasonable to speak of the [H2n-1On-1]+ fragments. According to the position of OH, the structures form two groups. In one group, OH acts exclusively as the proton acceptor in H-bonds with water molecules, thus being terminal in the chain-like structures; in the other group it is directly bonded to H3O and, as a proton donor, forms an H-bond with water molecule. Cluster cations do not tend to dissociate into the fragments. However, an external influence of ≤ 0.4 eV is sufficient for the cations of the first group to dissociate into a free OH radical and a protonated cluster H+(H2O)n-1. Extrapolation of the calculated adiabatic ionization potentials of the water clusters to n → ∞ provides a value of 8.6 eV, which can be considered as an estimation of the electron work function of water. This value is close to the experimental photoelectric thresholds of amorphous ice (8.7 ± 0.1 eV) and water (9.39 ± 0.3 eV). Solvation of the electron lowers the value, and an energy of 7 eV can be sufficient for initiating conductivity. This prediction is in accord with the experiment: irradiating ice with ultraviolet light of the photon energy 6.5-6.8 eV initiates photoconductivity, and hydrogen peroxide and H3O+ ions are observed.

Amide group anchored glucose oxidase based anodic catalysts for high performance enzymatic biofuel cell

NASA Astrophysics Data System (ADS)

Chung, Yongjin; Ahn, Yeonjoo; Kim, Do-Heyoung; Kwon, Yongchai

2017-01-01

A new enzyme catalyst is formed by fabricating gold nano particle (GNP)-glucose oxidase (GOx) clusters that are then attached to polyethyleneimine (PEI) and carbon nanotube (CNT) with cross-linkable terephthalaldehyde (TPA) (TPA/[CNT/PEI/GOx-GNP]). Especially, amide bonds belonging to TPA play an anchor role for incorporating rigid bonding among GNP, GOx and CNT/PEI, while middle size GNP is well bonded with thiol group of GOx to form strong GNP-GOx cluster. Those bonds are identified by chemical and electrochemical characterizations like XPS and cyclic voltammogram. The anchording effect of amide bonds induces fast electron transfer and strong chemical bonding, resulting in enhancements in (i) catalytic activity, (ii) amount of immobilized GOx and (ii) performance of enzymatic biofuel cell (EBC) including the catalyst. Regarding the catalytic activity, the TPA/[CNT/PEI/GOx-GNP] produces high electron transfer rate constant (6 s-1), high glucose sensitivity (68 μA mM-1 cm-2), high maximum current density (113 μA cm-2), low charge transfer resistance (17.0 Ω cm2) and long-lasting durability while its chemical structure is characterized by XPS confirming large portion of amide bond. In EBC measurement, it has high maximum power density (0.94 mW cm-2) compatible with catalytic acitivity measurements.

Unusually short chalcogen bonds involving organoselenium: insights into the Se-N bond cleavage mechanism of the antioxidant ebselen and analogues.

PubMed

Thomas, Sajesh P; Satheeshkumar, K; Mugesh, Govindasamy; Guru Row, T N

2015-04-27

Structural studies on the polymorphs of the organoselenium antioxidant ebselen and its derivative show the potential of organic selenium to form unusually short Se⋅⋅⋅O chalcogen bonds that lead to conserved supramolecular recognition units. Se⋅⋅⋅O interactions observed in these polymorphs are the shortest such chalcogen bonds known for organoselenium compounds. The FTIR spectral evolution characteristics of this interaction from solution state to solid crystalline state further validates the robustness of this class of supramolecular recognition units. The strength and electronic nature of the Se⋅⋅⋅O chalcogen bonds were explored using high-resolution X-ray charge density analysis and atons-in-molecules (AIM) theoretical analysis. A charge density study unravels the strong electrostatic nature of Se⋅⋅⋅O chalcogen bonding and soft-metal-like behavior of organoselenium. An analysis of the charge density around Se-N and Se-C covalent bonds in conjunction with the Se⋅⋅⋅O chalcogen bonding modes in ebselen and its analogues provides insights into the mechanism of drug action in this class of organoselenium antioxidants. The potential role of the intermolecular Se⋅⋅⋅O chalcogen bonding in forming the intermediate supramolecular assembly that leads to the bond cleavage mechanism has been proposed in terms of electron density topological parameters in a series of molecular complexes of ebselen with reactive oxygen species (ROS). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The π-Tetrel Bond and its Influence on Hydrogen Bonding and Proton Transfer.

PubMed

Wei, Yuanxin; Li, Qingzhong; Scheiner, Steve

2018-03-19

The positive region that lies above the plane of F 2 TO (T=C and Si) interacts with malondialdehyde (MDA), which contains an intramolecular H-bond. The T atom of F 2 TO can lie either in the MDA molecular plane, forming a T⋅⋅⋅O tetrel bond, or F 2 TO can stack directly above MDA in a parallel arrangement. The former structure is more stable than the latter, and in either case, F 2 SiO engages in a much stronger interaction than does F 2 CO, reaching nearly 200 kJ mol -1 . The π-tetrel bond strengthens/weakens the MDA H-bond when the bond is formed to the hydroxyl/carbonyl group of MDA, and causes an accompanying inhibition/promotion of proton transfer within this H-bond; this effect is stronger for F 2 SiO. These same aspects can be tuned by substituents placed on any of the C atoms of MDA, although their effects are not fully correlated with the electron-withdrawing or electron-releasing properties of the substituent. A new type of π-π tetrel bond occurs when the π-hole on the T atom of F 2 TO approaches the middle carbon atom of MDA from above, and a similar configuration is also found between F 2 TO and benzene. Evidence for extensive C⋅⋅⋅C π-π tetrel bonding in crystal materials is presented. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Diffusion bonding of Ti-48Ni-2Mn-2Nb (at.%)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Godfrey, S.P.; Strangwood, M.; Threadgill, P.L.

The diffusion bonding behavior of Ti-48at. % Al-2at. % Mn-2at. %Nb has been studied as a function of temperature (in the range 1,200--1,350C), time (15--45 minutes) and starting microstructure (lamellar, duplex and near {gamma}) at constant bonding pressure of 10 MPa. It was found, that under the above conditions, small twin related {gamma} grains, approximately 10-20 {mu}m in size, nucleated at the original interface and grew into the matrix forming a double necklace grain structure. Particles of {alpha}{sub 2} were observed around the interface, the formation of {alpha}{sub 2} particles was believed to be related to oxygen partitioning and stabilizationmore » effects from dissolved oxide films during the bonding process. Evidence for this mechanism was obtained from parallel electron energy loss spectroscopy (PEELS), which identified oxygen partitioning in the (X2) particles. For the fully lamellar structure bonded at 1,250 C for 45 minutes the failure strength of the bond was found to be 250 MPa, approximately 50 MPa lower than the failure strength of the base material.« less

Bone bonding strength of diamond-structured porous titanium-alloy implants manufactured using the electron beam-melting technique.

PubMed

Hara, Daisuke; Nakashima, Yasuharu; Sato, Taishi; Hirata, Masanobu; Kanazawa, Masayuki; Kohno, Yusuke; Yoshimoto, Kensei; Yoshihara, Yusuke; Nakamura, Akihiro; Nakao, Yumiko; Iwamoto, Yukihide

2016-02-01

The present study examined the bone bonding strength of diamond-structured porous titanium-alloy (Porous-Ti-alloy) manufactured using the electron beam-melting technique in comparison with fiber mesh-coated or rough-surfaced implants. Cylindrical implants with four different pore sizes (500, 640, 800, and 1000μm) of Porous-Ti-alloy, titanium fiber mesh (FM), and surfaces roughened by titanium arc spray (Ti-spray) were implanted into the distal femur of rabbits. Bone bonding strength and histological bone ingrowth were evaluated at 4 and 12weeks after implantation. The bone bonding strength of Porous-Ti-alloy implants (640μm pore size) increased over time from 541.4N at 4weeks to 704.6N at 12weeks and was comparable to that of FM and Ti-spray implants at both weeks. No breakage of the porous structure after mechanical testing was found with Porous-Ti-alloy implants. Histological bone ingrowth that increased with implantation time occurred along the inner structure of Porous-Ti-alloy implants. There was no difference in bone ingrowth in Porous-Ti-alloy implants with pore sizes among 500, 640, and 800μm; however, less bone ingrowth was observed with the 1000μm pore size. These results indicated Porous-Ti-alloy implants with pore size under 800μm provided biologically active and mechanically stable surface for implant fixation to bone, and had potential advantages for weight bearing orthopedic implants such as acetabular cups. Copyright © 2015 Elsevier B.V. All rights reserved.

Reactive carbon-chain molecules: synthesis of 1-diazo-2,4-pentadiyne and spectroscopic characterization of triplet pentadiynylidene (H-C[triple bond]C-:C-C[triple bond]C-H).

PubMed

Bowling, Nathan P; Halter, Robert J; Hodges, Jonathan A; Seburg, Randal A; Thomas, Phillip S; Simmons, Christopher S; Stanton, John F; McMahon, Robert J

2006-03-15

1-Diazo-2,4-pentadiyne (6a), along with both monodeuterio isotopomers 6b and 6c, has been synthesized via a route that proceeds through diacetylene, 2,4-pentadiynal, and 2,4-pentadiynal tosylhydrazone. Photolysis of diazo compounds 6a-c (lambda > 444 nm; Ar or N2, 10 K) generates triplet carbenes HC5H (1) and HC5D (1-d), which have been characterized by IR, EPR, and UV/vis spectroscopy. Although many resonance structures contribute to the resonance hybrid for this highly unsaturated carbon-chain molecule, experiment and theory reveal that the structure is best depicted in terms of the dominant resonance contributor of penta-1,4-diyn-3-ylidene (diethynylcarbene, H-C[triple bond]C-:C-C[triple bond]C-H). Theory predicts an axially symmetric (D(infinity h)) structure and a triplet electronic ground state for 1 (CCSD(T)/ANO). Experimental IR frequencies and isotope shifts are in good agreement with computed values. The triplet EPR spectrum of 1 (absolute value(D/hc) = 0.6157 cm(-1), absolute value(E/hc) = 0.0006 cm(-1)) is consistent with an axially symmetric structure, and the Curie law behavior confirms that the triplet state is the ground state. The electronic absorption spectrum of 1 exhibits a weak transition near 400 nm with extensive vibronic coupling. Chemical trapping of triplet HC5H (1) in an O2-doped matrix affords the carbonyl oxide 16 derived exclusively from attack at the central carbon.

Synthesis, structure, and bonding of BaTl4. Size effects on encapsulation of cations in electron-poor metal networks.

PubMed

Dai, Jing-Cao; Gupta, Shalabh; Corbett, John D

2011-01-03

The synthesis, structure, and bonding of BaTl(4) are described [C2/m, Z = 4, a = 12.408(3), b = 5.351(1), c = 10.383(2) Å, β = 116.00(3)°]. Pairs of edge-sharing Tl pentagons are condensed to generate a network of pentagonal biprisms along b that encapsulate Ba atoms. Alternating levels of prisms along c afford six more bifunctional Tl atoms about the waists of the biprisms, giving Ba a coordination number of 16. Each Tl atom is bonded to five to seven other Tl atoms and to three to five Ba atoms. There is also strong evidence that Hg substitutes preferentially in the shared edges of the Tl biprisms in BaHg(0.80)Tl(3.20) to generate more strongly bound Hg(2) dimers. Cations that are too small relative to the dimensions of the surrounding polyanionic network make this BaTl(4) structure (and for SrIn(4) and perhaps EuIn(4) as well) one stable alternative to tetragonal BaAl(4)-type structures in which cations are bound in larger hexagon-faced nets, as for BaIn(4) and SrGa(4). Characteristic condensation and augmentation of cation-centered prismatic units is common among many relatively cation- and electron-poor, polar derivatives of Zintl phases gain stability. At the other extreme, the large family of Frank-Kasper phases in which the elements exhibit larger numbers of bonded neighbors are sometimes referred to as orbitally rich.

Local structural aspects of metal-metal transition in IrTe2 from x-ray PDF

NASA Astrophysics Data System (ADS)

Yu, Runze; Abeykoon, Milinda; Zhou, Haidong; Yin, Weiguo; Bozin, Emil S.

Evolution of local atomic structure across the metal-metal transition in IrTe2 is explored by pair distribution function (PDF) analysis of x-ray total scattering data over 80 K

Role of composition, bond covalency, and short-range order in the disordering of stannate pyrochlores by swift heavy ion irradiation

NASA Astrophysics Data System (ADS)

Tracy, Cameron L.; Shamblin, Jacob; Park, Sulgiye; Zhang, Fuxiang; Trautmann, Christina; Lang, Maik; Ewing, Rodney C.

2016-08-01

A2S n2O7 (A =Nd ,Sm,Gd,Er,Yb,and Y) materials with the pyrochlore structure were irradiated with 2.2 GeV Au ions to systematically investigate disordering of this system in response to dense electronic excitation. Structural modifications were characterized, over multiple length scales, by transmission electron microscopy, x-ray diffraction, and Raman spectroscopy. Transformations to amorphous and disordered phases were observed, with disordering dominating the structural response of materials with small A -site cation ionic radii. Both the disordered and amorphous phases were found to possess weberite-type local ordering, differing only in that the disordered phase exhibits a long-range, modulated arrangement of weberite-type structural units into an average defect-fluorite structure, while the amorphous phase remains fully aperiodic. Comparison with the behavior of titanate and zirconate pyrochlores showed minimal influence of the high covalency of the Sn-O bond on this phase behavior. An analytical model of damage accumulation was developed to account for simultaneous amorphization and recrystallization of the disordered phase during irradiation.

Local atomic structure inheritance in Ag{sub 50}Sn{sub 50} melt

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bai, Yanwen; Bian, Xiufang, E-mail: xfbian@sdu.edu.cn; Qin, Jingyu

2014-01-28

Local structure inheritance signatures were observed during the alloying process of the Ag{sub 50}Sn{sub 50} melt, using high-temperature X-ray diffraction and ab initio molecular dynamics simulations. The coordination number N{sub m} around Ag atom is similar in the alloy and in pure Ag melts (N{sub m} ∼ 10), while, during the alloying process, the local structure around Sn atoms rearranges. Sn-Sn covalent bonds were substituted by Ag-Sn chemical bonds, and the total coordination number around Sn increases by about 70% as compared with those in the pure Sn melt. Changes in the electronic structure of the alloy have been studied by Agmore » and Sn K-edge X-ray absorption spectroscopy, as well as by calculations of the partial density of states. We propose that a leading mechanism for local structure inheritance in Ag{sub 50}Sn{sub 50} is due to s-p dehybridization of Sn and to the interplay between Sn-s and Ag-d electrons.« less

Method of bonding a conductive layer on an electrode of an electrochemical cell

DOEpatents

Bowker, J.C.; Singh, P.

1989-08-29

A dense, electronically conductive interconnection layer is bonded onto a porous, tubular, electronically conductive air electrode structure, optionally supported by a ceramic support, by (A) providing an air electrode surface, (B) forming on a selected portion of the electrode surface, without the use of pressure, particles of LaCrO[sub 3] doped with an element selected from the group consisting of Sr, Mg, Ca, Ba, Co, and mixtures thereof, where the particles have a deposit on their surface comprising calcium oxide and chromium oxide; (C) heating the particles with the oxide surface deposit in an oxidizing atmosphere at from 1,300 C to 1,550 C, without the application of pressure, to provide a dense, sintered, interconnection material bonded to the air electrode, where calcium and chromium from the surface deposit are incorporated into the structure of the LaCrO[sub 3]. A solid electrolyte layer can be applied to the uncovered portion of the air electrode, and a fuel electrode can be applied to the solid electrolyte, to provide an electrochemical cell. 4 figs.

Method of bonding a conductive layer on an electrode of an electrochemical cell

DOEpatents

Bowker, Jeffrey C.; Singh, Prabhakar

1989-01-01

A dense, electronically conductive interconnection layer 26 is bonded onto a porous, tubular, electronically conductive air electrode structure 16, optionally supported by a ceramic support 22, by (A) providing an air electrode surface, (B) forming on a selected portion of the electrode surface 24, without the use of pressure, particles of LaCrO.sub.3 doped with an element selected from the group consisting of Sr, Mg, Ca, Ba, Co, and mixtures thereof, where the particles have a deposit on their surface comprising calcium oxide and chromium oxide; (C) heating the particles with the oxide surface deposit in an oxidizing atmosphere at from 1,300.degree. C. to 1,550.degree. C., without the application of pressure, to provide a dense, sintered, interconnection material 26 bonded to the air electrode 16, where calcium and chromium from the surface deposit are incorporated into the structure of the LaCrO.sub.3. A solid electrolyte layer 18 can be applied to the uncovered portion of the air electrode, and a fuel electrode 20 can be applied to the solid electrolyte, to provide an electrochemical cell 10.

Pulsed EPR measurements on reaction rate constants for addition of photo-generated radicals to double bonds of diethyl fumarate and diethyl maleate

NASA Astrophysics Data System (ADS)

Takahashi, Hirona; Hagiwara, Kenta; Kawai, Akio

2016-11-01

Addition reaction of photo-generated radicals to double bonds of diethyl fumarate (deF) and diethyl maleate (deM), which are geometrical isomers, was studied by means of time-resolved- (TR-) and pulsed-electron paramagnetic resonance (EPR). Analysis of TR-EPR spectra indicates that adduct radicals from deF and deM should have the same structure. The double bonds of these monomers are converted to single ones by addition reaction, which allows hindered internal rotation to give the same structure of adduct radical. The rate constants for addition reaction of photo-generated radicals were determined by Stern-Volmer analysis of the decay time of electron spin-echo intensity of these radicals measured by the pulsed EPR method. Rate constants for deF were found to be larger than those for deM. This relation is in good consistent with efficiency of polymerisation of deF and deM. Experimentally determined rate constants were evaluated by introducing the addition reaction model on the basis of two important factors enthalpy and polar effects.

Theoretical study of structure, bonding, and electronic behavior of novel sandwich complexes Os3(C6H6) n ( n = 1, 2)

NASA Astrophysics Data System (ADS)

Zhou, K.; Zhao, C. B.; Huang, W. D.

2017-11-01

The correlations between structural and electronic properties of the monolayer cluster Os3 and sandwich complexes of Os3(C6H6) n ( n = 1, 2) were studied with density functional theory. Every Os adopts η2 fashion to coordinate with C6H6 in Os3(C6H6), while every Os adopts η2 and η1 fashion to coordinate with below and above C6H6 rings in Os3(C6H6)2. η2 fashion is σ donation and π back bond, and η1 fashion belong to σ bond. The first binding energy between Os3 and below C6H6 ring is-114.23 kJ/mol, which is weaker than the second binding energy with-174.16 kJ/mol between Os3(C6H6) and above C6H6 ring. The reason is that the change of spin multiplicity is different, which leads the symmetry of Os3(C6H6)2 to be broken.

Structural and electronic properties of armchair graphene nanoribbons under uniaxial strain

NASA Astrophysics Data System (ADS)

Qu, Li-Hua; Zhang, Jian-Min; Xu, Ke-Wei; Ji, Vincent

2014-02-01

We theoretically investigate the structures, relative stabilities and electronic properties of the armchair graphene nanoribbons (AGNRs) under uniaxial strain via first-principles calculations. The results show that, although each bond length decreases (increases) with increasing compression (tension) strain especially for the axial bonds a1, a4 and a7, the ribbon geometrical width d increases (decreases) with increasing compression (tension) strain due to the rotation of the zigzag bonds a2, a3, a5 and a6. For each nanoribbon, as expected, the lowest average energy corresponds to the unstrained state and the larger contract (elongate) deformation corresponds to the higher average energy. At a certain strain, the average energy increases with decreasing the ribbon width n. The average energy increases quadratically with the absolute value of the uniaxial strain, showing an elastic behavior. The dependence of the band gap on the strain is sensitive to the ribbon width n which can be classified into three distinct families n=3I, 3I+1 and 3I+2, where I is an integer. The ribbon width leads to oscillatory band gaps due to quantum confinement effect.

A theoretical investigation on Cu/Ag/Au bonding in XH2P⋯MY(X = H, CH3, F, CN, NO2; M = Cu, Ag, Au; Y = F, Cl, Br, I) complexes

NASA Astrophysics Data System (ADS)

Wang, Zhaoxu; Liu, Yi; Zheng, Baishu; Zhou, Fengxiang; Jiao, Yinchun; Liu, Yuan; Ding, XunLei; Lu, Tian

2018-05-01

Intermolecular interaction of XH2P...MY (X = H, CH3, F, CN, NO2; M = Cu, Ag, Au; Y = F, Cl, Br, I) complexes was investigated by means of an ab initio method. The molecular interaction energies are in the order Ag < Cu < Au and increased with the decrease of RP...M. Interaction energies are strengthened when electron-donating substituents X connected to XH2P, while electron-withdrawing substituents produce the opposite effect. The strongest P...M bond was found in CH3H2P...AuF with -70.95 kcal/mol, while the weakest one was found in NO2H2P...AgI with -20.45 kcal/mol. The three-center/four-electron (3c/4e) resonance-type of P:-M-:Y hyperbond was recognized by the natural resonance theory and the natural bond orbital analysis. The competition of P:M-Y ↔ P-M:Y resonance structures mainly arises from hyperconjugation interactions; the bond order of bP-M and bM-Y is in line with the conservation of the idealized relationship bP-M + bM-Y ≈ 1. In all MF-containing complexes, P-M:F resonance accounted for a larger proportion which leads to the covalent characters for partial ionicity of MF. The interaction energies of these Cu/Ag/Au complexes are basically above the characteristic values of the halogen-bond complexes and close to the observed strong hydrogen bonds in ionic hydrogen-bonded species.

Electronic structure of the alkyne-bridged dicobalt hexacarbonyl complex Co(2) micro-C(2)H(2) (CO)(6): evidence for singlet diradical character and implications for metal-metal bonding.

PubMed

Platts, James A; Evans, Gareth J S; Coogan, Michael P; Overgaard, Jacob

2007-08-06

A series of ab initio calculations are presented on the alkyne-bridged dicobalt hexacarbonyl cluster Co2 micro-C2H2 (CO)6, indicating that this compound has substantial multireference character, which we interpret as evidence of singlet diradical behavior. As a result, standard theoretical methods such as restricted Hartree-Fock (RHF) or Kohn-Sham (RKS) density functional theory cannot properly describe this compound. We have therefore used complete active space (CAS) methods to explore the bonding in and spectroscopic properties of Co2 micro-C2H2 (CO)6. CAS methods identify significant population of a Co-Co antibonding orbital, along with Co-pi* back-bonding, and a relatively large singlet-triplet energy splitting. Analysis of the electron density and related quantities, such as energy densities and atomic overlaps, indicates a small but significant amount of covalent bonding between cobalt centers.

Structural instability in polyacene: A projector quantum Monte Carlo study

NASA Astrophysics Data System (ADS)

Srinivasan, Bhargavi; Ramasesha, S.

1998-04-01

We have studied polyacene within the Hubbard model to explore the effect of electron correlations on the Peierls' instability in a system marginally away from one dimension. We employ the projector quantum Monte Carlo method to obtain ground-state estimates of the energy and various correlation functions. We find strong similarities between polyacene and polyacetylene which can be rationalized from the real-space valence-bond arguments of Mazumdar and Dixit. Electron correlations tend to enhance the Peierls' instability in polyacene. This enhancement appears to attain a maximum at U/t~3.0, and the maximum shifts to larger values when the alternation parameter is increased. The system shows no tendency to destroy the imposed bond-alternation pattern, as evidenced by the bond-bond correlations. The cis distortion is seen to be favored over the trans distortion. The spin-spin correlations show that undistorted polyacene is susceptible to a spin-density-wave distortion for large interaction strength. The charge-charge correlations indicate the absence of a charge-density-wave distortion for the parameters studied.

Regioselectivity of enzymatic and photochemical single electron transfer promoted carbon-carbon bond fragmentation reactions of tetrameric lignin model compounds.

PubMed

Cho, Dae Won; Latham, John A; Park, Hea Jung; Yoon, Ung Chan; Langan, Paul; Dunaway-Mariano, Debra; Mariano, Patrick S

2011-04-15

New types of tetrameric lignin model compounds, which contain the common β-O-4 and β-1 structural subunits found in natural lignins, have been prepared and carbon-carbon bond fragmentation reactions of their cation radicals, formed by photochemical (9,10-dicyanoanthracene) and enzymatic (lignin peroxidase) SET-promoted methods, have been explored. The results show that cation radical intermediates generated from the tetrameric model compounds undergo highly regioselective C-C bond cleavage in their β-1 subunits. The outcomes of these processes suggest that, independent of positive charge and odd-electron distributions, cation radicals of lignins formed by SET to excited states of sensitizers or heme-iron centers in enzymes degrade selectively through bond cleavage reactions in β-1 vs β-O-4 moieties. In addition, the findings made in the enzymatic studies demonstrate that the sterically large tetrameric lignin model compounds undergo lignin peroxidase-catalyzed cleavage via a mechanism involving preliminary formation of an enzyme-substrate complex.

Thioarsenides: A case for long-range Lewis acid-base-directed van der Waals interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibbs, Gerald V.; Wallace, Adam F.; Downs, R. T.

2011-04-01

Electron density distributions, bond paths, Laplacian and local energy density properties have been calculated for a number of As4Sn (n = 3,4,5) thioarsenide molecular crystals. On the basis of the distributions, the intramolecular As-S and As-As interactions classify as shared bonded interactions and the intermolecular As-S, As-As and S-S interactions classify as closed-shell van der Waals bonded interactions. The bulk of the intermolecular As-S bond paths link regions of locally concentrated electron density (Lewis base regions) with aligned regions of locally depleted electron density (Lewis acid regions) on adjacent molecules. The paths are comparable with intermolecular paths reported for severalmore » other molecular crystals that link aligned Lewis base and acid regions in a key-lock fashion, interactions that classified as long range Lewis acid-base directed van der Waals interactions. As the bulk of the intermolecular As-S bond paths (~70%) link Lewis acid-base regions on adjacent molecules, it appears that molecules adopt an arrangement that maximizes the number of As-S Lewis acid-base intermolecular bonded interactions. The maximization of the number of Lewis acid-base interactions appears to be connected with the close-packed array adopted by molecules: distorted cubic close-packed arrays are adopted for alacránite, pararealgar, uzonite, realgar and β-AsS and the distorted hexagonal close-packed arrays adopted by α- and β-dimorphite. A growth mechanism is proposed for thioarsenide molecular crystals from aqueous species that maximizes the number of long range Lewis acid-base vdW As-S bonded interactions with the resulting directed bond paths structuralizing the molecules as a molecular crystal.« less

Strength design of Zr(x)Ti(x)Hf(x)Nb(x)Mo(x) alloys based on empirical electron theory of solids and molecules

NASA Astrophysics Data System (ADS)

Li, Y. K.; Chen, Y. W.; Cheng, X. W.; Wu, C.; Cheng, B.

2018-05-01

In this paper, the valence electron structure parameters of Zr(x)Ti(x)Hf(x)Nb(x)Mo(x) alloys were calculated based on the empirical electron theory of solids and molecules (EET), and their performance through these parameters were predicted. Subsequently, the alloys with special valence electron structure parameters were prepared byarc melting. The hardness and high-temperature mechanical properties were analyzed to verify the prediction. Research shows that the influence of shared electron number nA on the strongest bond determines the strength of these alloys and the experiments are consistent with the theoretical prediction.

OsB 2 and RuB 2, ultra-incompressible, hard materials: First-principles electronic structure calculations

NASA Astrophysics Data System (ADS)

Chiodo, S.; Gotsis, H. J.; Russo, N.; Sicilia, E.

2006-07-01

Recently it has been reported that osmium diboride has an unusually large bulk modulus combined with high hardness, and consequently is a most interesting candidate as an ultra-incompressible and hard material. The electronic and structural properties of the transition metal diborides OsB 2 and RuB 2 have been calculated within the local density approximation (LDA). It is shown that the high hardness is the result of covalent bonding between transition metal d states and boron p states in the orthorhombic structure.

Optoelectronic tuning of organoborylazadipyrromethenes via effective electronegativity at the metalloid center.

PubMed

Berhe, Seare A; Rodriguez, Marco T; Park, Eunsol; Nesterov, Vladimir N; Pan, Hongjun; Youngblood, W Justin

2014-03-03

Organoborylazadipyrromethenes were synthesized from free base and fluoroborylazadipyrromethenes and characterized with regard to their structural and electronic properties. B-N bond lengths, along with photophysical and redox behavior, appear dependent on the effective electronegativity at the boron atom as tuned by its substituents, with stronger electronegativity correlating to a shorter B-N bond length, red-shifted absorbance, enhanced fluorescence lifetime and yield, and positively shifted redox potentials.

NMR structural study of the prototropic equilibrium in solution of Schiff bases as model compounds.

PubMed

Ortegón-Reyna, David; Garcías-Morales, Cesar; Padilla-Martínez, Itzia; García-Báez, Efren; Aríza-Castolo, Armando; Peraza-Campos, Ana; Martínez-Martínez, Francisco

2013-12-31

An NMR titration method has been used to simultaneously measure the acid dissociation constant (pKa) and the intramolecular NHO prototropic constant ΔKNHO on a set of Schiff bases. The model compounds were synthesized from benzylamine and substituted ortho-hydroxyaldehydes, appropriately substituted with electron-donating and electron-withdrawing groups to modulate the acidity of the intramolecular NHO hydrogen bond. The structure in solution was established by 1H-, 13C- and 15N-NMR spectroscopy. The physicochemical parameters of the intramolecular NHO hydrogen bond (pKa, ΔKNHO and ΔΔG°) were obtained from 1H-NMR titration data and pH measurements. The Henderson-Hasselbalch data analysis indicated that the systems are weakly acidic, and the predominant NHO equilibrium was established using Polster-Lachmann δ-diagram analysis and Perrin model data linearization.

Electron transfer across multiple hydrogen bonds: the case of ureapyrimidinedione-substituted vinyl ruthenium and osmium complexes.

PubMed

Pichlmaier, Markus; Winter, Rainer F; Zabel, Manfred; Zális, Stanislav

2009-04-08

Ruthenium and osmium complexes 2a,b and 3a,b featuring the N-4,6-dioxo-5,5-dibutyl- or the N-4,6-dioxo-5,5-di-(2-propenyl)-1,4,5,6-tetrahydropyrimidin-2-yl-N'(4-ethenylphenyl)-urea ligand dimerize by a self-complementary quadruply hydrogen-bonding donor/donor/acceptor/acceptor (DDAA) motif. We provide evidence that the dimeric structures are maintained in nonpolar solvents and in 0.1 M NBu(4)PF(6)/CH(2)Cl(2) supporting electrolyte solution. All complexes are reversibly oxidized in two consecutive two-electron oxidations (DeltaE(1/2) approximately = 500 mV) without any discernible potential splitting for the oxidation of the individual hydrogen-bridged redox active moieties. IR and UV/vis/NIR spectroelectrochemistry show a one-step conversion of the neutral to the dication without any discernible features of an intermediate monooxidized radical cation. Oxidation-induced IR changes of the NH and CO groups that are involved in hydrogen bonding are restricted to the styryl-bonded urea NH function. IR band assignments are aided by quantum chemical calculations. Our experimental findings clearly show that, at least in the present systems, the ureapyrimidinedione (Upy) DDAA hydrogen-bonding motif does not support electron transfer. The apparent reason is that neither of the hydrogen-bonding functionalities contributes to the occupied frontier levels. This results in nearly degenerate pairs of MOs representing the in-phase and out-of-phase combinations of the individual monomeric building blocks.

Elimination of the azeotropic point of acetone and methanol by 1,3-dimethylimidazolium dimethylphosphate: an ab initio calculation study.

PubMed

Yu, Guangren; Liu, Xiaomin; Zhang, Xiaochun; Chen, Xiaochun; Liu, Zhiping; Abdeltawab, Ahmed A

2017-03-01

1,3-Dimethylimidazolium dimethylphosphate ([C 1 mim][DMP]) was observed experimentally to be able to eliminate the atmospheric azeotropic point of acetone and methanol, which is an important azeotrope generally encountered in furfural production and the Fischer-Tropsch process. Here, we employed ab initio calculation to understand the underlying mechanism of [C 1 mim][DMP] in eliminating the azeotropic point of acetone and methanol. Structure, energy and interaction in binary-, ternary- and quaternary-clusters composed of methanol, acetone, [C 1 mim] + or/and [DMP]‾ were calculated. The σ-hole, AIM and NBO analyses were performed to understand intermolecular interaction with electron density, electron occupancy, charge transfer and molecular orbital interaction. Hydrogen bond interaction plays a key role in azeotropic point elimination; due to the much stronger hydrogen bond interaction between methanol and [C 1 mim][DMP] than that between acetone and [C 1 mim][DMP], [C 1 mim][DMP] prefers to interact with methanol rather than acetone, and the original interaction between methanol and acetone is separated by [C 1 mim][DMP]. The hydrogen bond is from the orbital interaction between O lone-pair-electron orbitals of the hydrogen bond acceptor and σ * (C-H) or σ * (O-H) anti-bonding orbitals of the hydrogen bond donor, where remarkable electron or charge transfer occurs. These theoretical calculation results are in agreement with the experimental observation that [C 1 mim][DMP] eliminates the azeotropic point of methanol and acetone. This work shows that ab initio calculation may be employed to rationalize the design or synthesis of ionic liquids for separating azeotropes. Graphical Abstract Elimination of azeotropic point of acetone and methanol by [C 1 mim][DMP].

The structure of Na{sub 3}SbTe{sub 3}: How ionic and covalent bonding forces work together

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Jianhua; Miller, G.J.

1994-12-01

The compound Na{sub 3}SbTe{sub 3} has been synthesized from the elements and characterized by single crystal X-ray diffraction. Na{sub 3}SbTe{sub 3} is cubic, crystallizing in the cP28 structure type (isomorphous with Na{sub 3}AsS{sub 3}); space group P2{sub 1}3 (No. 198); a=9.6114(9) {angstrom}; Z = 4; R1 = 0.0324; wR2 = 0.0561 (I {le} 2{sigma}(I)). The structure consists of isolated sodium cations and trigonal pyramidal [SbTe{sub 3}]{sup {minus}3} anions with a Sb-Te bond length of 2.787(1) {angstrom} and a Te-Sb-Te bond angle of 100.0(1){degrees}. The structure is related to both the Li{sub 3}Bi and K{sub 3}AsS{sub 4}-type structures. Both lattice energymore » and semiempirical electronic structure calculations are utilized to evaluate various local and long-range structural aspects of this Zintl phase.« less

Electronic hybridisation implications for the damage-tolerance of thin film metallic glasses

PubMed Central

Schnabel, Volker; Jaya, B. Nagamani; Köhler, Mathias; Music, Denis; Kirchlechner, Christoph; Dehm, Gerhard; Raabe, Dierk; Schneider, Jochen M.

2016-01-01

A paramount challenge in materials science is to design damage-tolerant glasses. Poisson’s ratio is commonly used as a criterion to gauge the brittle-ductile transition in glasses. However, our data, as well as results in the literature, are in conflict with the concept of Poisson’s ratio serving as a universal parameter for fracture energy. Here, we identify the electronic structure fingerprint associated with damage tolerance in thin film metallic glasses. Our correlative theoretical and experimental data reveal that the fraction of bonds stemming from hybridised states compared to the overall bonding can be associated with damage tolerance in thin film metallic glasses. PMID:27819318

Electronic hybridisation implications for the damage-tolerance of thin film metallic glasses.

PubMed

Schnabel, Volker; Jaya, B Nagamani; Köhler, Mathias; Music, Denis; Kirchlechner, Christoph; Dehm, Gerhard; Raabe, Dierk; Schneider, Jochen M

2016-11-07

A paramount challenge in materials science is to design damage-tolerant glasses. Poisson's ratio is commonly used as a criterion to gauge the brittle-ductile transition in glasses. However, our data, as well as results in the literature, are in conflict with the concept of Poisson's ratio serving as a universal parameter for fracture energy. Here, we identify the electronic structure fingerprint associated with damage tolerance in thin film metallic glasses. Our correlative theoretical and experimental data reveal that the fraction of bonds stemming from hybridised states compared to the overall bonding can be associated with damage tolerance in thin film metallic glasses.

Hydrogen bond and halogen bond inside the carbon nanotube

NASA Astrophysics Data System (ADS)

Wang, Weizhou; Wang, Donglai; Zhang, Yu; Ji, Baoming; Tian, Anmin

2011-02-01

The hydrogen bond and halogen bond inside the open-ended single-walled carbon nanotubes have been investigated theoretically employing the newly developed density functional M06 with the suitable basis set and the natural bond orbital analysis. Comparing with the hydrogen or halogen bond in the gas phase, we find that the strength of the hydrogen or halogen bond inside the carbon nanotube will become weaker if there is a larger intramolecular electron-density transfer from the electron-rich region of the hydrogen or halogen atom donor to the antibonding orbital of the X-H or X-Hal bond involved in the formation of the hydrogen or halogen bond and will become stronger if there is a larger intermolecular electron-density transfer from the electron-rich region of the hydrogen or halogen atom acceptor to the antibonding orbital of the X-H or X-Hal bond. According to the analysis of the molecular electrostatic potential of the carbon nanotube, the driving force for the electron-density transfer is found to be the negative electric field formed in the carbon nanotube inner phase. Our results also show that the X-H bond involved in the formation of the hydrogen bond and the X-Hal bond involved in the formation of the halogen bond are all elongated when encapsulating the hydrogen bond and halogen bond within the carbon nanotube, so the carbon nanotube confinement may change the blue-shifting hydrogen bond and the blue-shifting halogen bond into the red-shifting hydrogen bond and the red-shifting halogen bond. The possibility to replace the all electron nanotube-confined calculation by the simple polarizable continuum model is also evaluated.

Origin of the 900 cm{sup −1} broad double-hump OH vibrational feature of strongly hydrogen-bonded carboxylic acids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Hoozen, Brian L.; Petersen, Poul B.

2015-03-14

Medium and strong hydrogen bonds are common in biological systems. Here, they provide structural support and can act as proton transfer relays to drive electron and/or energy transfer. Infrared spectroscopy is a sensitive probe of molecular structure and hydrogen bond strength but strongly hydrogen-bonded structures often exhibit very broad and complex vibrational bands. As an example, strong hydrogen bonds between carboxylic acids and nitrogen-containing aromatic bases commonly display a 900 cm{sup −1} broad feature with a remarkable double-hump structure. Although previous studies have assigned this feature to the OH, the exact origin of the shape and width of this unusualmore » feature is not well understood. In this study, we present ab initio calculations of the contributions of the OH stretch and bend vibrational modes to the vibrational spectrum of strongly hydrogen-bonded heterodimers of carboxylic acids and nitrogen-containing aromatic bases, taking the 7-azaindole—acetic acid and pyridine—acetic acid dimers as examples. Our calculations take into account coupling between the OH stretch and bend modes as well as how both of these modes are affected by lower frequency dimer stretch modes, which modulate the distance between the monomers. Our calculations reproduce the broadness and the double-hump structure of the OH vibrational feature. Where the spectral broadness is primarily caused by the dimer stretch modes strongly modulating the frequency of the OH stretch mode, the double-hump structure results from a Fermi resonance between the out of the plane OH bend and the OH stretch modes.« less

Radical O-O coupling reaction in diferrate-mediated water oxidation studied using multireference wave function theory.

PubMed

Kurashige, Yuki; Saitow, Masaaki; Chalupský, Jakub; Yanai, Takeshi

2014-06-28

The O-O (oxygen-oxygen) bond formation is widely recognized as a key step of the catalytic reaction of dioxygen evolution from water. Recently, the water oxidation catalyzed by potassium ferrate (K2FeO4) was investigated on the basis of experimental kinetic isotope effect analysis assisted by density functional calculations, revealing the intramolecular oxo-coupling mechanism within a di-iron(vi) intermediate, or diferrate [Sarma et al., J. Am. Chem. Soc., 2012, 134, 15371]. Here, we report a detailed examination of this diferrate-mediated O-O bond formation using scalable multireference electronic structure theory. High-dimensional correlated many-electron wave functions beyond the one-electron picture were computed using the ab initio density matrix renormalization group (DMRG) method along the O-O bond formation pathway. The necessity of using large active space arises from the description of complex electronic interactions and varying redox states both associated with two-center antiferromagnetic multivalent iron-oxo coupling. Dynamic correlation effects on top of the active space DMRG wave functions were additively accounted for by complete active space second-order perturbation (CASPT2) and multireference configuration interaction (MRCI) based methods, which were recently introduced by our group. These multireference methods were capable of handling the double shell effects in the extended active space treatment. The calculations with an active space of 36 electrons in 32 orbitals, which is far over conventional limitation, provide a quantitatively reliable prediction of potential energy profiles and confirmed the viability of the direct oxo coupling. The bonding nature of Fe-O and dual bonding character of O-O are discussed using natural orbitals.

Some Comments on Topological Approaches to the π-Electron Currents in Conjugated Systems.

PubMed

Dickens, Timothy K; Gomes, José A N F; Mallion, Roger B

2011-11-08

Within the past two years, three sets of independent authors (Mandado, Ciesielski et al., and Randić) have proposed methods in which π-electron currents in conjugated systems are estimated by invoking the concept of circuits of conjugation. These methods are here compared with ostensibly similar approaches published more than 30 years ago by two of the present authors (Gomes and Mallion) and (likewise independently) by Gayoso. Patterns of bond currents and ring currents computed by these methods for the nonalternant isomer of coronene that was studied by Randić are also systematically compared with those calculated by the Hückel-London-Pople-McWeeny (HLPM) "topological" approach and with the ab initio, "ipso-centric" current-density maps of Balaban et al. These all agree that a substantial diamagnetic π-electron current flows around the periphery of the selected structure (which could be thought of as a "perturbed" [18]-annulene), and consideration is given to the differing trends predicted by these several methods for the π-electron currents around its central six-membered ring and in its internal bonds. It is observed that, for any method in which calculated π-electron currents respect Kirchhoff's Laws of current conservation at a junction, consideration of bond currents-as an alternative to the more-traditional ring currents-can give a different insight into the magnetic properties of conjugated systems. However, provided that charge/current conservation is guaranteed-or Kirchhoff's First Law holds for bond currents instead of the more-general current-densities-then ring currents represent a more efficient way of describing the molecular reaction to the external magnetic field: ring currents are independent quantities, while bond currents are not.

Structures of Mo2Oy- and Mo2Oy (y=2, 3, and 4) studied by anion photoelectron spectroscopy and density functional theory calculations.

PubMed

Yoder, Bruce L; Maze, Joshua T; Raghavachari, Krishnan; Jarrold, Caroline Chick

2005-03-01

The competitive structural isomers of the Mo(2)O(y) (-)Mo(2)O(y) (y=2, 3, and 4) clusters are investigated using a combination of anion photoelectron (PE) spectroscopy and density functional theory calculations. The PE spectrum and calculations for MoO(3) (-)MoO(3) are also presented to show the level of agreement to be expected between the spectra and calculations. For MoO(3) (-) and MoO(3), the calculations predict symmetric C(3v) structures, an adiabatic electron affinity of 3.34 eV, which is above the observed value 3.17(2) eV. However, there is good agreement between observed and calculated vibrational frequencies and band profiles. The PE spectra of Mo(2)O(2) (-) and Mo(2)O(3) (-) are broad and congested, with partially resolved vibrational structure on the lowest energy bands observed in the spectra. The electron affinities (EA(a)s) of the corresponding clusters are 2.24(2) and 2.33(7) eV, respectively. Based on the calculations, the most stable structure of Mo(2)O(2) (-) is Y shaped, with the two Mo atoms directly bonded. Assignment of the Mo(2)O(3) (-) spectrum is less definitive, but a O-Mo-O-Mo-O structure is more consistent with overall electronic structure observed in the spectrum. The PE spectrum of Mo(2)O(4) (-) shows cleanly resolved vibrational structure and electronic bands, and the EA of the corresponding Mo(2)O(4) is determined to be 2.13(4) eV. The structure most consistent with the observed spectrum has two oxygen bridge bonds between the Mo atoms.

Barrier-free proton transfer in the valence anion of 2'-deoxyadenosine-5'-monophosphate. II. A computational study.

PubMed

Kobyłecka, Monika; Gu, Jiande; Rak, Janusz; Leszczynski, Jerzy

2008-01-28

The propensity of four representative conformations of 2(')-deoxyadenosine-5(')-monophosphate (5(')-dAMPH) to bind an excess electron has been studied at the B3LYP6-31++G(d,p) level. While isolated canonical adenine does not support stable valence anions in the gas phase, all considered neutral conformations of 5(')-dAMPH form adiabatically stable anions. The type of an anionic 5(')-dAMPH state, i.e., the valence, dipole bound, or mixed (valence/dipole bound), depends on the internal hydrogen bond(s) pattern exhibited by a particular tautomer. The most stable anion results from an electron attachment to the neutral syn-south conformer. The formation of this anion is associated with a barrier-free proton transfer triggered by electron attachment and the internal rotation around the C4(')-C5(') bond. The adiabatic electron affinity of the a_south-syn anion is 1.19 eV, while its vertical detachment energy is 1.89 eV. Our results are compared with the photoelectron spectrum (PES) of 5(')-dAMPH(-) measured recently by Stokes et al., [J. Chem. Phys. 128, 044314 (2008)]. The computational VDE obtained for the most stable anionic structure matches well with the experimental electron binding energy region of maximum intensity. A further understanding of DNA damage might require experimental and computational studies on the systems in which purine nucleotides are engaged in hydrogen bonding.

Barrier-free proton transfer in the valence anion of 2'-deoxyadenosine-5'-monophosphate. II. A computational study

NASA Astrophysics Data System (ADS)

Kobyłecka, Monika; Gu, Jiande; Rak, Janusz; Leszczynski, Jerzy

2008-01-01

The propensity of four representative conformations of 2'-deoxyadenosine-5'-monophosphate (5'-dAMPH) to bind an excess electron has been studied at the B3LYP /6-31++G(d,p) level. While isolated canonical adenine does not support stable valence anions in the gas phase, all considered neutral conformations of 5'-dAMPH form adiabatically stable anions. The type of an anionic 5'-dAMPH state, i.e., the valence, dipole bound, or mixed (valence/dipole bound), depends on the internal hydrogen bond(s) pattern exhibited by a particular tautomer. The most stable anion results from an electron attachment to the neutral syn-south conformer. The formation of this anion is associated with a barrier-free proton transfer triggered by electron attachment and the internal rotation around the C4'-C5' bond. The adiabatic electron affinity of the a&barbelow;south-syn anion is 1.19eV, while its vertical detachment energy is 1.89eV. Our results are compared with the photoelectron spectrum (PES) of 5'-dAMPH- measured recently by Stokes et al., [J. Chem. Phys. 128, 044314 (2008)]. The computational VDE obtained for the most stable anionic structure matches well with the experimental electron binding energy region of maximum intensity. A further understanding of DNA damage might require experimental and computational studies on the systems in which purine nucleotides are engaged in hydrogen bonding.

Investigation of secondary school, undergraduate, and graduate learners' mental models of ionic bonding

NASA Astrophysics Data System (ADS)

Coll, Richard K.; Treagust, David F.

2003-05-01

Secondary school, undergraduate, and graduate level learners' mental models of bonding in ionic substances were explored using an interview protocol that involved the use of physical substances and a focus card containing depictions of ionic bonding and structure. Teachers and faculty from the teaching institutions were interviewed to contextualize teaching models within the educational setting for the inquiry. These data resulted in two socially negotiated consensus teaching models and a series of criterial attributes for these models: the essential qualities, all of which must be negotiated, if the model is used in a way that is acceptable to scientists. The secondary school learners see ionic bonding as consisting of attraction of oppositely charged species that arise from the transfer of electrons driven by the desire of atoms to obtain an octet of electrons. The undergraduates see the lattice structure as a key component of ionic substances and quickly identified specific ionic lattices for the physical prompts used as probes. The graduates also identified strongly with ionic lattices, were less likely to focus on particular ionic structures, and had a stronger appreciation for the notion of the ionic-covalent continuum. The research findings suggest that learners at all educational levels harbor a number of alternative conceptions and prefer to use simple mental models. These findings suggest that teachers and university faculty need to provide stronger links between the detailed nature of a model and its intended purpose.

H2O incorporation in the phosphorene/a-SiO2 interface: a first-principles study

NASA Astrophysics Data System (ADS)

Scopel, Wanderlã L.; Souza, Everson S.; Miwa, R. H.

2017-02-01

Based on first-principles calculations, we investigate (i) the energetic stability and electronic properties of single-layer phosphorene (SLP) adsorbed on an amorphous SiO2 surface (SLP/a-SiO2), and (ii) the further incorporation of water molecules at the phosphorene/a-SiO2 interface. In (i), we find that the phosphorene sheet binds to a-SiO2 through van der Waals interactions, even in the presence of oxygen vacancies on the surface. The SLP/a-SiO2 system presents a type-I band alignment, with the valence (conduction) band maximum (minimum) of the phosphorene lying within the energy gap of the a-SiO2 substrate. The structure and the surface-potential corrugations promote the formation of electron-rich and electron-poor regions on the phosphorene sheet and at the SLP/a-SiO2 interface. Such charge density puddles are strengthened by the presence of oxygen vacancies in a-SiO2. In (ii), because of the amorphous structure of the surface, we consider a number of plausible geometries for H2O embedded in the SLP/a-SiO2 interface. There is an energetic preference for the formation of hydroxyl (OH) groups on the a-SiO2 surface. Meanwhile, in the presence of oxygenated water or interstitial oxygen in the phosphorene sheet, we observe the formation of metastable OH bonded to the phosphorene, and the formation of energetically stable P-O-Si chemical bonds at the SLP/a-SiO2 interface. Further x-ray absorption spectra simulations are performed, which aim to provide additional structural/electronic information on the oxygen atoms forming hydroxyl groups or P-O-Si chemical bonds at the interface region.

H2O incorporation in the phosphorene/a-SiO2 interface: a first-principles study.

PubMed

Scopel, Wanderlã L; Souza, Everson S; Miwa, R H

2017-02-22

Based on first-principles calculations, we investigate (i) the energetic stability and electronic properties of single-layer phosphorene (SLP) adsorbed on an amorphous SiO 2 surface (SLP/a-SiO 2 ), and (ii) the further incorporation of water molecules at the phosphorene/a-SiO 2 interface. In (i), we find that the phosphorene sheet binds to a-SiO 2 through van der Waals interactions, even in the presence of oxygen vacancies on the surface. The SLP/a-SiO 2 system presents a type-I band alignment, with the valence (conduction) band maximum (minimum) of the phosphorene lying within the energy gap of the a-SiO 2 substrate. The structure and the surface-potential corrugations promote the formation of electron-rich and electron-poor regions on the phosphorene sheet and at the SLP/a-SiO 2 interface. Such charge density puddles are strengthened by the presence of oxygen vacancies in a-SiO 2 . In (ii), because of the amorphous structure of the surface, we consider a number of plausible geometries for H 2 O embedded in the SLP/a-SiO 2 interface. There is an energetic preference for the formation of hydroxyl (OH) groups on the a-SiO 2 surface. Meanwhile, in the presence of oxygenated water or interstitial oxygen in the phosphorene sheet, we observe the formation of metastable OH bonded to the phosphorene, and the formation of energetically stable P-O-Si chemical bonds at the SLP/a-SiO 2 interface. Further x-ray absorption spectra simulations are performed, which aim to provide additional structural/electronic information on the oxygen atoms forming hydroxyl groups or P-O-Si chemical bonds at the interface region.

Bonding and structure of copper nitrenes.

PubMed

Cundari, Thomas R; Dinescu, Adriana; Kazi, Abul B

2008-11-03

Copper nitrenes are of interest as intermediates in the catalytic aziridination of olefins and the amination of C-H bonds. However, despite advances in the isolation and study of late-transition-metal multiply bonded complexes, a bona fide structurally characterized example of a terminal copper nitrene has, to our knowledge, not been reported. In anticipation of such a report, terminal copper nitrenes are studied from a computational perspective. The nitrene complexes studied here are of the form (beta-diketiminate)Cu(NPh). Density functional theory (DFT), complete active space self-consistent-field (CASSCF) electronic structure techniques, and hybrid quantum mechanical/molecular mechanical (QM/MM) methods are employed to study such species. While DFT methods indicate that a triplet (S = 1) is the ground state, CASSCF calculations indicate that a singlet (S = 0) is the ground state, with only a small energy gap between the singlet and triplet. Moreover, the ground-state (open-shell) singlet copper nitrene is found to be highly multiconfigurational (i.e., biradical) and to possess a bent geometry about the nitrene nitrogen, contrasting with the linear nitrene geometry of the triplet copper nitrenes. CASSCF calculations also reveal the existence of a closed-shell singlet state with some degree of multiple bonding character for the copper-nitrene bond.

Structure and Bonding in CE5- (E=Al-Tl) Clusters: Planar Tetracoordinate Carbon versus Pentacoordinate Carbon.

PubMed

Ravell, Estefanía; Jalife, Said; Barroso, Jorge; Orozco-Ic, Mesías; Hernández-Juárez, Gerardo; Ortiz-Chi, Filiberto; Pan, Sudip; Cabellos, José Luis; Merino, Gabriel

2018-03-24

The structure, bonding, and stability of clusters with the empirical formula CE 5 - (E=Al-Tl) have been analyzed by means of high-level computations. The results indicate that, whereas aluminum and gallium clusters have C 2v structures with a planar tetracoordinate carbon (ptC), their heavier homologues prefer three-dimensional C 4v forms with a pentacoordinate carbon center over the ptC one. The reason for such a preference is a delicate balance between the interaction energy of the fifth E atom with CE 4 and the distortion energy. Moreover, bonding analysis shows that the ptC systems can be better described as CE 4 - , with 17-valence electrons interacting with E. The ptC core in these systems exhibits double aromatic (both σ and π) behavior, but the σ contribution is dominating. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reversible Twisting of Primary Amides via Ground State N-C(O) Destabilization: Highly Twisted Rotationally Inverted Acyclic Amides.

PubMed

Meng, Guangrong; Shi, Shicheng; Lalancette, Roger; Szostak, Roman; Szostak, Michal

2018-01-17

Since the seminal studies by Pauling in 1930s, planarity has become the defining characteristic of the amide bond. Planarity of amides has central implications for the reactivity and chemical properties of amides of relevance to a range of chemical disciplines. While the vast majority of amides are planar, nonplanarity has a profound effect on the properties of the amide bond, with the most common method to restrict the amide bond relying on the incorporation of the amide function into a rigid cyclic ring system. In a major departure from this concept, here, we report the first class of acyclic twisted amides that can be prepared, reversibly, from common primary amides in a single, operationally trivial step. Di-tert-butoxycarbonylation of the amide nitrogen atom yields twisted amides in which the amide bond exhibits nearly perpendicular twist. Full structural characterization of a range of electronically diverse compounds from this new class of twisted amides is reported. Through reactivity studies we demonstrate unusual properties of the amide bond, wherein selective cleavage of the amide bond can be achieved by a judicious choice of the reaction conditions. Through computational studies we evaluate structural and energetic details pertaining to the amide bond deformation. The ability to selectively twist common primary amides, in a reversible manner, has important implications for the design and application of the amide bond nonplanarity in structural chemistry, biochemistry and organic synthesis.

Degradation reaction of Diazo reactive black 5 dye with copper (II) sulfate catalyst in thermolysis treatment.

PubMed

Lau, Yen-Yie; Wong, Yee-Shian; Ang, Tze-Zhang; Ong, Soon-An; Lutpi, Nabilah Aminah; Ho, Li-Ngee

2018-03-01

The theme of present research demonstrates performance of copper (II) sulfate (CuSO 4 ) as catalyst in thermolysis process to treat reactive black 5 (RB 5) dye. During thermolysis without presence of catalyst, heat was converted to thermal energy to break the enthalpy of chemical structure bonding and only 31.62% of color removal. With CuSO 4 support as auxiliary agent, the thermally cleaved molecular structure was further destabilized and reacted with CuSO 4 . Copper ions functioned to delocalize the coordination of π of the lone paired electron in azo bond, C=C bond of the sp 2 carbon to form C-C of the sp 3 amorphous carbon in benzene and naphthalene. Further, the radicals of unpaired electrons were stabilized and RB 5 was thermally decomposed to methyl group. Zeta potential measurement was carried out to analyze the mechanism of RB 5 degradation and measurement at 0 mV verified the critical chemical concentration (CCC) (0.7 g/L copper (II) sulfate), as the maximum 92.30% color removal. The presence of copper (II) sulfate catalyst has remarkably increase the RB 5 dye degradation as the degradation rate constant without catalyst, k 1 is 6.5224 whereas the degradation rate constant with catalyst, k 2 is 25.6810. This revealed the correlation of conversion of thermal energy from heat to break the chemical bond strength, subsequent fragmentation of RB 5 dye molecular mediated by copper (II) sulfate catalyst. The novel framework on thermolysis degradation of molecular structure of RB 5 with respect to the bond enthalpy and interfacial intermediates decomposition with catalyst reaction were determined.

Lie algebraic approach to valence bond theory of π-electron systems: a preliminary study of excited states

NASA Astrophysics Data System (ADS)

Paldus, J.; Li, X.

1992-10-01

Following a brief outline of various developments and exploitations of the unitary group approach (UGA), and its extension referred to as Clifford algebra UGA (CAUGA), in molecular electronic structure calculations, we present a summary of a recently introduced implementation of CAUGA for the valence bond (VB) method based on the Pariser-Parr-Pople (PPP)-type Hamiltonian. The existing applications of this PPP-VB approach have been limited to groundstates of various π-electron systems or, at any rate, to the lowest states of a given multiplicity. In this paper the method is applied to the low-lying excited states of several archetypal models, namely cyclobutadiene and benzene, representing antiaromatic and aromatic systems, hexatriene, representing linear polyenic systems and, finally, naphthalene, representing polyacenes.

Charge Carriers Modulate the Bonding of Semiconductor Nanoparticle Dopants As Revealed by Time-Resolved X-ray Spectroscopy

DOE PAGES

Hassan, Asra; Zhang, Xiaoyi; Liu, Xiaohan; ...

2017-08-28

Understanding the electronic structure of doped semiconductors is essential to realize advancements in electronics and in the rational design of nanoscale devices. Here, we report the results of time-resolved X-ray absorption studies on copper-doped cadmium sulfide nanoparticles that provide an explicit description of the electronic dynamics of the dopants. The interaction of a dopant ion and an excess charge carrier is unambiguously observed via monitoring the oxidation state. The experimental data combined with DFT calculations demonstrate that dopant bonding to the host matrix is modulated by its interaction with charge carriers. Additionally, the transient photoluminescence and the kinetics of dopantmore » oxidation reveal the presence of two types of surface-bound ions that create mid-gap states.« less

Charge Carriers Modulate the Bonding of Semiconductor Nanoparticle Dopants As Revealed by Time-Resolved X-ray Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hassan, Asra; Zhang, Xiaoyi; Liu, Xiaohan

Understanding the electronic structure of doped semiconductors is essential to realize advancements in electronics and in the rational design of nanoscale devices. Here, we report the results of time-resolved X-ray absorption studies on copper-doped cadmium sulfide nanoparticles that provide an explicit description of the electronic dynamics of the dopants. The interaction of a dopant ion and an excess charge carrier is unambiguously observed via monitoring the oxidation state. The experimental data combined with DFT calculations demonstrate that dopant bonding to the host matrix is modulated by its interaction with charge carriers. Additionally, the transient photoluminescence and the kinetics of dopantmore » oxidation reveal the presence of two types of surface-bound ions that create mid-gap states.« less

A quantum informational approach for dissecting chemical reactions

NASA Astrophysics Data System (ADS)

Duperrouzel, Corinne; Tecmer, Paweł; Boguslawski, Katharina; Barcza, Gergely; Legeza, Örs; Ayers, Paul W.

2015-02-01

We present a conceptionally different approach to dissect bond-formation processes in metal-driven catalysis using concepts from quantum information theory. Our method uses the entanglement and correlation among molecular orbitals to analyze changes in electronic structure that accompany chemical processes. As a proof-of-principle example, the evolution of nickel-ethene bond-formation is dissected, which allows us to monitor the interplay of back-bonding and π-donation along the reaction coordinate. Furthermore, the reaction pathway of nickel-ethene complexation is analyzed using quantum chemistry methods, revealing the presence of a transition state. Our study supports the crucial role of metal-to-ligand back-donation in the bond-forming process of nickel-ethene.

Cyclo-biphenalenyl biradicaloid molecular materials: conformation, rearrangement, magnetism, and thermochromism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Jingsong; Sumpter, Bobby G; Meunier, Vincent

2010-01-01

Cyclo-biphenalenyl biradicaloid molecular materials with chair- and boat-conformations are studied by restricted and broken-symmetry DFT using the M06 family of meta-GGA functionals. The global minima of these molecular materials are magnetically silent due to the sigma-bond connecting the two phenalenyls, while the sigma-bond may undergo low-barrier sigmatropic rearrangements via pi-pi bonded paramagnetic intermediates. The validation of theory is performed for the chair-conformation by comparing the sigma-bonded structures and the rearrangement barriers with experimental data. The boat-conformation is then studied using the validated functional. The electronic spectra of both chair- and boat-conformations are calculated and their applications in thermochromism are discussed.

Influence of charged defects on the interfacial bonding strength of tantalum- and silver-doped nanograined TiO2.

PubMed

Azadmanjiri, Jalal; Wang, James; Berndt, Christopher C; Kapoor, Ajay; Zhu, De Ming; Ang, Andrew S M; Srivastava, Vijay K

2017-05-17

A nano-grained layer including line defects was formed on the surface of a Ti alloy (Ti alloy , Ti-6Al-4V ELI). Then, the micro- and nano-grained Ti alloy with the formation of TiO 2 on its top surface was coated with a bioactive Ta layer with or without incorporating an antibacterial agent of Ag that was manufactured by magnetron sputtering. Subsequently, the influence of the charged defects (the defects that can be electrically charged on the surface) on the interfacial bonding strength and hardness of the surface system was studied via an electronic model. Thereby, material systems of (i) Ta coated micro-grained titanium alloy (Ta/MGTi alloy ), (ii) Ta coated nano-grained titanium alloy (Ta/NGTi alloy ), (iii) TaAg coated micro-grained titanium alloy (TaAg/MGTi alloy ) and (iv) TaAg coated nano-grained titanium alloy (TaAg/NGTi alloy ) were formed. X-ray photoelectron spectroscopy was used to probe the electronic structure of the micro- and nano-grained Ti alloy , and so-formed heterostructures. The thin film/substrate interfaces exhibited different satellite peak intensities. The satellite peak intensity may be related to the interfacial bonding strength and hardness of the surface system. The interfacial layer of TaAg/NGTi alloy exhibited the highest satellite intensity and maximum hardness value. The increased bonding strength and hardness in the TaAg/NGTi alloy arises due to the negative core charge of the dislocations and neighbor space charge accumulation, as well as electron accumulation in the created semiconductor phases of larger band gap at the interfacial layer. These two factors generate interfacial polarization and enhance the satellite intensity. Consequently, the interfacial bonding strength and hardness of the surface system are improved by the formation of mixed covalent-ionic bonding structures around the dislocation core area and the interfacial layer. The bonding strength relationship by in situ XPS on the metal/TiO 2 interfacial layer may be examined with other noble metals and applied in diverse fields.

Density functional theory investigation of the geometric and electronic structures of [UO2(H2O)m(OH)n](2 - n) (n + m = 5).

PubMed

Ingram, Kieran I M; Häller, L Jonas L; Kaltsoyannis, Nikolas

2006-05-28

Gradient corrected density functional theory has been used to calculate the geometric and electronic structures of the family of molecules [UO2(H2O)m(OH)n](2 - n) (n + m = 5). Comparisons are made with previous experimental and theoretical structural and spectroscopic data. r(U-O(yl)) is found to lengthen as water molecules are replaced by hydroxides in the equatorial plane, and the nu(sym) and nu(asym) uranyl vibrational wavenumbers decrease correspondingly. GGA functionals (BP86, PW91 and PBE) are generally found to perform better for the cationic complexes than for the anions. The inclusion of solvent effects using continuum models leads to spurious low frequency imaginary vibrational modes and overall poorer agreement with experimental data for nu(sym) and nu(asym). Analysis of the molecular orbital structure is performed in order to trace the origin of the lengthening and weakening of the U-O(yl) bond as waters are replaced by hydroxides. No evidence is found to support previous suggestions of a competition for U 6d atomic orbitals in U-O(yl) and U-O(hydroxide)pi bonding. Rather, the lengthening and weakening of U-O(yl) is attributed to reduced ionic bonding generated in part by the sigma-donating ability of the hydroxide ligands.

Dipole and Coulomb forces in electron capture dissociation and electron transfer dissociation mass spectroscopy.

PubMed

Świerszcz, Iwona; Skurski, Piotr; Simons, Jack

2012-02-23

Ab initio electronic structure calculations were performed on a doubly charged polypeptide model H(+)-Lys(Ala)(19)-CO-CH(NH(2))-CH(2)-SS-CH(2)-(NH(2))CH-CO-(Ala)(19)-Lys-H(+) consisting of a C-terminal protonated Lys followed by a 19-Ala α-helix with a 20th Ala-like unit whose side chain is linked by a disulfide bond to a corresponding Ala-like unit connected to a second 19-Ala α-helix terminated by a second C-terminal-protonated Lys. The Coulomb potentials arising from the two charged Lys residues and dipole potentials arising from the two oppositely directed 72 D dipoles of the α-helices act to stabilize the SS bond's σ* orbital. The Coulomb potentials provide stabilization of 1 eV, while the two large dipoles generate an additional 4 eV. Such stabilization allows the SS σ* orbital to attach an electron and thereby generate disulfide bond cleavage products. Although calculations are performed only on SS bond cleavage, discussion of N-C(α) bond cleavage caused by electron attachment to amide π* orbitals is also presented. The magnitudes of the stabilization energies as well as the fact that they arise from Coulomb and dipole potentials are supported by results on a small model system consisting of a H(3)C-SS-CH(3) molecule with positive and negative fractional point charges to its left and right designed to represent (i) two positive charges ca. 32 Å distant (i.e., the two charged Lys sites of the peptide model) and (ii) two 72 D dipoles (i.e., the two α-helices). Earlier workers suggested that internal dipole forces in polypeptides could act to guide incoming free electrons (i.e., in electron capture dissociation (ECD)) toward the positive end of the dipole and thus affect the branching ratios for cleaving various bonds. Those workers argued that, because of the huge mass difference between an anion donor and a free electron, internal dipole forces would have a far smaller influence over the trajectory of a donor (i.e., in electron transfer dissociation (ETD)). The present findings suggest that, in addition to their effects on guiding electron or donor trajectories, dipole potentials (in combination with Coulomb potentials) also alter the energies of SS σ* and amide π* orbitals, which then affects the ability of these orbitals to bind an electron. Thus, both by trajectory-guiding and by orbital energy stabilization, Coulomb and dipole potentials can have significant influences on the branching ratios of ECD and ETC in which disulfide or N-C(α) bonds are cleaved. © 2012 American Chemical Society

Bond angle variations in XH3 [X = N, P, As, Sb, Bi]: the critical role of Rydberg orbitals exposed using a diabatic state model.

PubMed

Reimers, Jeffrey R; McKemmish, Laura K; McKenzie, Ross H; Hush, Noel S

2015-10-14

Ammonia adopts sp(3) hybridization (HNH bond angle 108°) whereas the other members of the XH3 series PH3, AsH3, SbH3, and BiH3 instead prefer octahedral bond angles of 90-93°. We use a recently developed general diabatic description for closed-shell chemical reactions, expanded to include Rydberg states, to understand the geometry, spectroscopy and inversion reaction profile of these molecules, fitting its parameters to results from Equation of Motion Coupled-Cluster Singles and Doubles (EOM-CCSD) calculations using large basis sets. Bands observed in the one-photon absorption spectrum of NH3 at 18.3 eV, 30 eV, and 33 eV are reassigned from Rydberg (formally forbidden) double excitations to valence single-excitation resonances. Critical to the analysis is the inclusion of all three electronic states in which two electrons are placed in the lone-pair orbital n and/or the symmetric valence σ* antibonding orbital. An illustrative effective two-state diabatic model is also developed containing just three parameters: the resonance energy driving the high-symmetry planar structure, the reorganization energy opposing it, and HXH bond angle in the absence of resonance. The diabatic orbitals are identified as sp hybrids on X; for the radical cations XH3(+) for which only 2 electronic states and one conical intersection are involved, the principle of orbital following dictates that the bond angle in the absence of resonance is acos(-1/5) = 101.5°. The multiple states and associated multiple conical intersection seams controlling the ground-state structure of XH3 renormalize this to acos[3 sin(2)(2(1/2)atan(1/2))/2 - 1/2] = 86.7°. Depending on the ratio of the resonance energy to the reorganization energy, equilibrium angles can vary from these limiting values up to 120°, and the anomalously large bond angle in NH3 arises because the resonance energy is unexpectedly large. This occurs as the ordering of the lowest Rydberg orbital and the σ* orbital swap, allowing Rydbergization to compresses σ* to significantly increase the resonance energy. Failure of both the traditional and revised versions of the valence-shell electron-pair repulsion (VSEPR) theory to explain the ground-state structures in simple terms is attributed to exclusion of this key physical interaction.

Dominance of broken bonds and nonbonding electrons at the nanoscale

NASA Astrophysics Data System (ADS)

Sun, Chang Q.

2010-10-01

Although they exist ubiquitously in human bodies and our surroundings, the impact of nonbonding lone electrons and lone electron pairs has long been underestimated. Recent progress demonstrates that: (i) in addition to the shorter and stronger bonds between under-coordinated atoms that initiate the size trends of the otherwise constant bulk properties when a substance turns into the nanoscale, the presence of lone electrons near to broken bonds generates fascinating phenomena that bulk materials do not demonstrate; (ii) the lone electron pairs and the lone pair-induced dipoles associated with C, N, O, and F tetrahedral coordination bonding form functional groups in biological, organic, and inorganic specimens. By taking examples of surface vacancy, atomic chain end and terrace edge states, catalytic enhancement, conducting-insulating transitions of metal clusters, defect magnetism, Coulomb repulsion at nanoscale contacts, Cu3C2H2 and Cu3O2 surface dipole formation, lone pair neutralized interface stress, etc, this article will focus on the development and applications of theory regarding the energetics and dynamics of nonbonding electrons, aiming to raise the awareness of their revolutionary impact to the society. Discussion will also extend to the prospective impacts of nonbonding electrons on mysteries such as catalytic enhancement and catalysts design, the density anomalies of ice and negative thermal expansion, high critical temperature superconductivity induced by B, C, N, O, and F, the molecular structures and functionalities of CF4 in anti-coagulation of synthetic blood, NO signaling, and enzyme telomeres, etc. Meanwhile, an emphasis is placed on the necessity and effectiveness of understanding the properties of substances from the perspective of bond and nonbond formation, dissociation, relaxation and vibration, and the associated energetics and dynamics of charge repopulation, polarization, densification, and localization. Finding and grasping the factors controlling the nonbonding states and making them of use in functional materials design and identifying their limitations will form, in the near future, a subject area of ``nonbonding electronics and energetics'', which could be even more challenging, fascinating, promising, and rewarding than dealing with core or valence electrons alone.