Si-O bonded interactions in silicate crystals and molecules: a comparison

Bond critical point, local kinetic energy density, G(rc), and local potential energy density, V(rc), properties of the electron density distributions, rho(r), calculated for silicates such as quartz and gas-phase molecules such as disiloxane are similar, indicating that the forces that govern the Si-O bonded interactions in silica are short-ranged and molecular-like. Using the G(rc)/rho(rc) ratio as a measure of bond character, the ratio increases as the Si-O bond length, the local electronic energy density, H(rc)= G(rc) + V(rc), and the coordination number of the Si atom decrease and as the accumulation of the electron density at the bond critical point, rho(rc), and the Laplacian, inverted Delta2 rho(rc), increase. The G(rc)/rho(rc) and H(rc)/rho(rc) ratios categorize the bonded interaction as observed for other second row atom M-O bonds into discrete categories with the covalent character of each of the M-O bonds increasing with the H(rc)/rho(rc) ratio. The character of the bond is examined in terms of the large net atomic charges conferred on the Si atoms comprising disiloxane, stishovite, quartz, and forsterite and the domains of localized electron density along the Si-O bond vectors and on the reflex side of the Si-O-Si angle together with the close similarity of the Si-O bonded interactions observed for a variety of hydroxyacid silicate molecules and a large number of silicate crystals. The bond critical point and local energy density properties of the electron density distribution indicate that the bond is an intermediate interaction between Al-O and P-O bonded interactions rather than being a closed-shell or a shared interaction.     

Effect of bond exchange rate on dynamics and mechanics of vitrimers

Thermoset polymers are classified amongst the most challenging materials to recycle due to the permanent crosslinks that increase their strength and stiffness compared to their thermoplastic counterparts. Vitrimers provide a promising route to achieve the recyclability of thermosets by implementing dynamic covalent bonds within the network. In this study, a hybrid molecular dynamics (MD)-Monte Carlo (MC) technique is used to simulate these adaptive networks constructed by a coarse-grained model. The model proposed in this work describes the dynamic nature of the covalent bonds while maintaining a constant crosslink density. As this framework also shows flexibility in accommodating various exchange reaction activation energy via adjusting the energy difference in MC step, the dynamic and mechanical properties of the vitrimer system are intensely affected by the number of successful bond exchanges happening at every step. In both rubbery and glassy regimes, lowering the energy barrier of the bond exchange reaction results in enhanced motion for the vitrimer segments. This enhanced mobility, in turn, directly affects the stress–strain relationship of these networks, where a higher number of exchanges results in larger deformation before fracture even at low temperatures. Furthermore, the stress distribution in vitrimers shows more homogenous distribution before failure than in the thermoset network.     

Direct and indirect causes of Fermi level pinning at the SiO/GaAs interface

The correlation between atomic bonding sites and the electronic structure of SiO on GaAs(001)-c(2x8)/(2x4) was investigated using scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and density functional theory (DFT). At low coverage, STM images reveal that SiO molecules bond Si end down; this is consistent with Si being undercoordinated and O being fully coordinated in molecular SiO. At approximately 5% ML (monolayer) coverage, multiple bonding geometries were observed. To confirm the site assignments from STM images, DFT calculations were used to estimate the total adsorption energies of the different bonding geometries as a function of SiO coverage. STS measurements indicated that SiO pins the Fermi level midgap at approximately 5% ML coverage. DFT calculations reveal that the direct causes of Fermi level pinning at the SiO GaAs(001)-(2x4) interface are a result of either local charge buildups or the generation of partially filled dangling bonds on Si atoms.     

Interaction of amino acids with gold and silver clusters

Binding of gold and silver clusters with amino acids (glycine and cysteine) was studied using density functional theory (DFT). Geometries of neutral, anionic, and cationic amino acids with Au3 and Ag3 clusters were optimized using the DFT-B3LYP approach. The mixed basis set used here was denoted by 6-31+G** (union or logical sum)LANL2DZ. This work demonstrated that the interaction of amino acids with gold and silver clusters is governed by two major bonding factors: (a) the anchoring N-Au(Ag), O-Au(Ag), and S-Au(Ag) bonds and (b) the nonconventional N-H...Au(Ag) and O-H...Au(Ag) hydrogen bonds. Among the three forms of amino acids, anionic ones exhibited the most tendency to interact with the Au and Ag clusters. Natural bond orbital analysis was performed to calculate charge transfer, natural population analysis, and Wiberg bond indices of the complexes. Atoms-in-molecules theory was also applied to determine the nature of interactions. It was shown that these bonds are partially electrostatic and partially covalent.     

Glucose interaction with Au,Ag, and Cu clusters: Theoretical investigation

Interactions of α‐D ‐glucose with gold, silver, and copper metal clusters are studied theoretically at the density functional theory (CAM‐B3LYP) and MP2 levels of theory, using trimer clusters as simple catalytic models for metal particles as well as investigating the effect of cluster charge by studying the interactions of cationic and anionic gold clusters with glucose. The bonding between α‐D ‐glucose and metal clusters occurs by two major bonding factors; the anchoring of M atoms (M = Cu, Ag, and Au) to the O atoms, and the unconventional M…H? O hydrogen bond. Depending on the charge of metal clusters, each of these bonds contributes significantly to the complexation. Binding energy calculations indicate that the silver cluster has the lowest and gold cluster has the highest affinity to interact with glucose. Natural bond orbital analysis is performed to calculate natural population analysis and charge transfers in the complexes. Quantum theory of atoms in molecules was also applied to interpret the nature of bonds. © 2012 Wiley Periodicals, Inc.     

X-ray photoelectron spectroscopy for detection of the different Si–O bonding states of silicon

X-ray photoelectron spectroscopy (XPS) was used to detect the bonding between a silica particle surface and attached silanes. In addition to the commonly recorded Si 2p spectrum, the Si 1 s level is also accessible when monochromatic Ag Lalpha X-rays are applied. Furthermore, the spectrum of the Si 1 s level shows a fine structure. After spectrum deconvolution, we assigned the fitted spectral peaks to Si-C bonds of the silanes and to the Si-O bonds of the silica network. The recorded Si 1 s spectra were deconvoluted into peaks originating from Si-C bonds and the Si-O-Si silica network. To check the results of spectrum deconvolution, several differently functionalized silanes containing stoichiometric amounts of heteroatoms were applied for silica surface modification. We conclude that spectra deconvolution of the Si 1 s signal is an appropriate means for quantification of surface attached silane molecules.     

The stability of titania‐silica interface

Silica is very often the catalyst support of choice for transition metal oxides such as titania, and specially anatase. Titania is an excellent absorber and photocatalyst for many organic molecules degradation. In order to understand the chemical nature of the interaction between titania and silica, we have performed a theoretical study using density functional theory aiming to elucidate the role on the stability of the interface of the specific type of interactions, H‐bonding, covalent bonding of the pristine surfaces, and covalent bonding after silicon and titanium ions interdiffusion. The calculations were carried out for hydrogen and oxygen terminated surface, comparing the bonding types and the forces acting along the interface. The interface dynamics was studied for interfaces under applied stress in order to elucidate their stability and failure limits. The shearing forces and the mechanisms of interface failure were determined. Interfaces with interdiffused Si and Ti ions were studied to improve the interface stabilization. The results demonstrate that high‐temperature treatment leading to formation of Si O Ti bonds at the interface is responsible for the formation of strong and flexible binding interaction between both oxides. At high strains, the Si O Ti interface failure is observed due to lattice mismatch between the SiO₂ and TiO₂. The failure is a result of forces acting orthogonal to the interface shearing. In case of hydrogen terminated surface, the interface binding is a result of hydrogen bond network. Such interface is fragile at moderate shearing forces along the applied strain. The hydrogen bond network decreases the elastic properties and flexibility of the interface. The SiO₂/TiO₂ interface is further stabilized by Si/Ti ion interdiffusion. The ionic interdiffusion process also increases the interface flexibility. Thus, in order to obtain more stable anatase photocatalyst supported on silica, the synthetic routes should favor silicon and titanium ions interdiffusion along the interface.     

Charge-shift bonding--a class of electron-pair bonds that emerges from valence bond theory and is supported by the electron localization function approach

This paper deals with a central paradigm of chemistry, the electron-pair bond. Valence bond (VB) theory and electron-localization function (ELF) calculations of 21 single bonds demonstrate that along the two classical bond families of covalent and ionic bonds, there exists a class of charge-shift bonds (CS bonds) in which the fluctuation of the electron pair density plays a dominant role. In VB theory, CS bonding manifests by way of a large covalent-ionic resonance energy, RE(CS), and in ELF by a depleted basin population with large variances (fluctuations). CS bonding is shown to be a fundamental mechanism that is necessary to satisfy the equilibrium condition, namely the virial ratio of the kinetic and potential energy contributions to the bond energy. The paper defines the atomic propensity and territory for CS bonding: Atoms (fragments) that are prone to CS bonding are compact electronegative and/or lone-pair-rich species. As such, the territory of CS bonding transcends considerations of static charge distribution, and involves: a) homopolar bonds of heteroatoms with zero static ionicity, b) heteropolar sigma and pi bonds of the electronegative and/or electron-pair-rich elements among themselves and to other atoms (e.g., the higher metalloids, Si, Ge, Sn, etc), c) all hypercoordinate molecules. Several experimental manifestations of charge-shift bonding are discussed, such as depleted bonding density, the rarity of ionic chemistry of silicon in condensed phases, and the high barriers of halogen-transfer reactions as compared to hydrogen-transfers.     

Three-center-two-electron and four-center-four-electron bonds. A study by electron charge density over the structure of methonium cations

We study the electronic density charge topology of CH(5)(+) species 1 (C(s)()), 2 (C(s)()), and 3 (C(2)(v)) at ab initio level using the theory of atoms in molecules developed by Bader. Despite the reports of previous studies concerning carbocationic species, the methane molecule is protonated at the carbon atom, which clearly shows its pentacoordination. In addition to the fact that hydrogen atoms in the methonium molecule behave in a very fluxional fashion and that the energy difference among the species 1, 2, and 3 are very low, is important to point out that two different topological situations can be defined on the basis of our study of the topology of the electronic charge density. Then, the species 1 and 2 present a three-center-two-electron (3c-2e) bond of singular characteristics as compared with other carbocationic species, but in the species 3, the absence of a 3c-2e bond is noteworthy. This structure can be characterized through the three bond critical points found, corresponding to saddle points on the path bonds between the C-H(2,3,5) that lie in the same plane. These nuclei define a four-center interaction where the electronic delocalization produced among the sigma(C-H) bonds provide a stabilization of the three C-H bonds involved in this interaction (the remaining two C-H bonds are similar to those belonging to the nonprotonated species). Our results show that bonding situations with a higher number of atom arrays are possible in protonated hydrocarbons.     

Orbital contributions to the molecular charge and energy density distributions in Co2(CO)8

For Co2(CO)8, the representative of a whole class of bridged cobalt complexes, the 18-electron rule predicts a direct metal-metal bond in addition to the metal-bridge bonds. By intuition, this bond should have bent-bond character. However, it is well-known from charge density analyses that no bond critical point exists in the corresponding spatial region. Otherwise, the energy density distribution points to a certain stabilizing contribution of this local area to the total molecular energy. It is shown that a partitioning of the total charge and energy densities into orbital contributions can lead to a deeper insight into complex bonding properties.     

Photoluminescent properties of novel rare earth organic-inorganic nanocomposite with TiO2 modified silica via double crosslinking units

A series of novel organic/inorganic rare earth (europium, terbium) hybrid materials through the coordination bond and covalent bond are synthesized and form an inorganic Si-O-Si by the sol-gel process. Mercapto-functionalized 4-mercaptobenzoic acid (MBA-Si) is obtained by using MBA and 3-(triethoxysilyl)-propyl isocyanate (TESPIC) as an organic bridge molecule, and then the carboxyl group of the precursor MBA-Si is used to modify the titanium dioxide, so as to sensitize the luminescence of rare earth ions. CdS-TiO(2) is added to observe the influence of photoluminescence. 3-mercaptopropyltrimethoxysilane (MPS) is also used to modify the CdS quantum dot and obtain MPS functionalized MPS-CdS nanocomposite. These multicomponent hybrids with double cross-linking siloxane (MBA-Si) covalently bonding MPS-CdS are characterized. Subsequently, 1,10-phenanthroline (Phen) and 2,2,-bipyridyl (Bipy) as the assistant ligands together with water molecules are introduced into the rare earth hybrid system. The FT-IR, X-ray diffraction, UV-Vis, thermogravimetry and especially the photoluminescence properties of them are studied in detail.     

Dimetalloendofullerene U(2)@C(60) has a U-U multiple bond consisting of sixfold one-electron-two-center bonds

Endohedral metallofullerenes (EMFs) have been extensively studied since their discovery in 1985. Metal-metal bonds, nevertheless, have never been explicitly observed in EMFs synthesized so far. In this contribution, we show by means of all-electron relativistic density functional computations that the dimetalloendofullerene, U(2)@C(60), has an unprecedented U-U multiple bond consisting solely of sixfold ferromagnetically coupled one-electron-two-center bonds with the electronic configuration (5fpi(u))(2)(5fsigma(g))(1)(5fdelta(g))(2)(5fphi(u))(1), which are dominated by the uranium 5f atomic orbitals. This bonding scheme is completely distinct from the metal-metal bonds discovered thus far in the d- and f-block polynuclear metal complexes. This finding initiates a connection of the metal-metal multiple bonding chemistry and the fullerene chemistry.     

Topology of charge density of flucytosine and related molecules and characteristics of their bond charge distributions

The molecular charge distribution of flucytosine (4-amino-5-fluoro-2-pyrimidone), uracil, 5-fluorouracil, and thymine was studied by means of density functional theory calculations (DFT). The resulting distributions were analyzed by means of the atoms in molecules (AIM) theory. Bonds were characterized through vectors formed with the charge density value, its Laplacian, and the bond ellipticity calculated at the bond critical point (BCP). Within each set of C=O, C-H, and N-H bonds, these vectors showed little dispersion. C-C bonds formed three different subsets, one with a significant degree of double bonding, a second corresponding to single bonds with a finite ellipticity produced by hyperconjugation, and a third one formed by a pure single bond. In N-C bonds, a decrease in bond length (an increase in double bond character) was not reflected as an increase in their ellipticity, as in all C-C bonds studied. It was also found that substitution influenced the N-C, C-O, and C-C bond ellipticity much more than density and its Laplacian at the BCP. The Laplacian of charge density pointed to the existence of both bonding and nonbonding maxima in the valence shell charge concentration of N, O, and F, while only bonding ones were found for the C atoms. The nonbonding maxima related to the sites for electrophilic attack and H bonding in O and N, while sites of nucleophilic attack were suggested by the holes in the valence shell of the C atoms of the carbonyl groups.     

The structure and chemical bonding in the N(2)-CuX and N(2)...XCu (X = F, Cl, Br) systems studied by means of the molecular orbital and Quantum Chemical Topology methods

Ab initio studies carried out at the MP2(full)/6-311+G(2df) and MP2(full)/aug-cc-pVTZ-PP computational levels reveals that dinitrogen (N(2)) and cuprous halides (CuX, X = F, Cl, Br) form three types of systems with the side-on and end-on coordination of N(2): N[triple bond]N-CuX (C(infinity v)), N(2)-CuX (C(2v)) stabilized by the donor-acceptor bonds and weak van der Waals complexes N(2)...XCu (C(2v)) with dominant dispersive forces. An electron density transfer between the N(2) and CuX depends on type of the N(2) coordination and a comparison of the NPA charges yields the [N[triple bond]N](delta+)-[CuX](delta-) and [N(2)](delta-)-[CuX](delta+) formula. According to the NBO analysis, the Cu-N coordinate bonds are governed by predominant LP(N2)-->sigma*(Cu-X) "2e-delocalization" in the most stable N[triple bond]N-CuX systems, meanwhile back donation LP(Cu)-->pi*(N-N) prevails in less stable N(2)-CuX molecules. A topological analysis of the electron density (AIM) presents single BCP between the Cu and N nuclei in the N[triple bond]N-CuX, two BCPs corresponding to two donor-acceptor Cu-N bonds in the N(2)-CuX and single BCP between electron density maximum of the N[triple bond]N bond and halogen nucleus in the van der Waals complexes N(2)...XCu. In all systems values of the Laplacian nabla(2)rho(r)(r(BCP)) are positive and they decrease following a trend of the complex stability i.e. N[triple bond]N-CuX (C(infinity v)) > N(2)-CuX (C(2v)) > N(2)...XCu (C(2v)). A topological analysis of the electron localization function (ELF) reveals strongly ionic bond in isolated CuF and a contribution of covalent character in the Cu-Cl and Cu-Br bonds. The donor-acceptor bonds Cu-N are characterized by bonding disynaptic basins V(Cu,N) with attractors localized at positions corresponding to slightly distorted lone pairs V(N) in isolated N(2). In the N[triple bond]N-CuX systems, there were no creation of any new bonding attractors in regions where classically the donor-acceptor bonds are expected and there is no sign of typical covalent bond Cu-N with the bonding pair. Calculations carried out for the N[triple bond]N-CuX reveal small polarization of the electron density in the N[triple bond]N bond, which is reflected by the bond polarity index being in range of 0.14 (F) to 0.11 (Cl).     

An Excursion from Normal to Inverted C?C Bonds Shows a Clear Demarcation between Covalent and Charge‐Shift C?C Bonds

What is the nature of the C? C bond? Valence bond and electron density computations of 16 C? C bonds show two families of bonds that flesh out as a phase diagram. One family, involving ethane, cyclopropane and so forth, is typified by covalent C? C bonding wherein covalent spin‐pairing accounts for most of the bond energy. The second family includes the inverted bridgehead bonds of small propellanes, where the bond is neither covalent nor ionic, but owes its existence to the resonance stabilization between the respective structures; hence a charge‐shift (CS) bond. The dual family also emerges from calculated and experimental electron density properties. Covalent C? C bonds are characterized by negative Laplacians of the density, whereas CS‐bonds display small or positive Laplacians. The positive Laplacian defines a region suffering from neighbouring repulsive interactions, which is precisely the case in the inverted bonding region. Such regions are rich in kinetic energy, and indeed the energy‐density analysis reveals that CS‐bonds are richer in kinetic energy than the covalent C? C bonds. The large covalent–ionic resonance energy is precisely the mechanism that lowers the kinetic energy in the bonding region and restores equilibrium bonding. Thus, different degrees of repulsive strain create two bonding families of the same chemical bond made from a single atomic constituent. It is further shown that the idea of repulsive strain is portable and can predict the properties of propellanes of various sizes and different wing substituents. Experimentally (M. Messerschmidt, S. Scheins, L. Bruberth, M. Patzel, G. Szeimies, C. Paulman, P. Luger, Angew. Chem. 2005 , 117, 3993–3997; Angew. Chem. Int. Ed. 2005 , 44, 3925–3928), the C? C bond families are beautifully represented in [1.1.1]propellane, where the inverted C? C is a CS‐bond, while the wings are made from covalent C? C bonds. What other manifestations can we expect from CS‐bonds? Answers from experiment have the potential of recharting the mental map of chemical bonding.     

Trigger bond analysis of nitroaromatic energetic materials using wiberg bond indices

The identification of trigger bonds, bonds that break to initiate explosive decomposition, using computational methods could help direct the development of novel, “green” and efficient high energy density materials (HEDMs). Comparing bond densities in energetic materials to reference molecules using Wiberg bond indices (WBIs) provides a relative scale for bond activation (%ΔWBIs) to assign trigger bonds in a set of 63 nitroaromatic conventional energetic molecules. Intramolecular hydrogen bonding interactions enhance contributions of resonance structures that strengthen, or deactivate, the C NO₂ trigger bonds and reduce the sensitivity of nitroaniline‐based HEDMs. In contrast, unidirectional hydrogen bonding in nitrophenols strengthens the bond to the hydrogen bond acceptor, but the phenol lone pairs repel and activate an adjacent nitro group. Steric effects, electron withdrawing groups and greater nitro dihedral angles also activate the C NO₂ trigger bonds. %ΔWBIs indicate that nitro groups within an energetic molecule are not all necessarily equally activated to contribute to initiation. %ΔWBIs generally correlate well with impact sensitivity, especially for HEDMs with intramolecular hydrogen bonding, and are a better measure of trigger bond strength than bond dissociation energies (BDEs). However, the method is less effective for HEDMs with significant secondary effects in the solid state. Assignment of trigger bonds using %ΔWBIs could contribute to understanding the effect of intramolecular interactions on energetic properties. © 2018 Wiley Periodicals, Inc.     

Investigating the quartz (1010)/water interface using classical and ab initio molecular dynamics

Two different terminations of the (1010) surface of quartz (α and β) interacting with water are simulated by classical (CMD) (using two different force fields) and ab initio molecular dynamics (AIMD) and compared with previously published X-ray reflectivity (XR) experiments. Radial distribution functions between hydroxyl and water show good agreement between AIMD and CMD using the ClayFF force field for both terminations. The Lopes et al. (Lopes, P. E. M.; Murashov, V.; Tazi, M.; Demchuk, E.; MacKerell, A. D. J. Phys. Chem. B2006, 110, 2782-2792) force field (LFF), however, underestimates the extent of hydroxyl-water hydrogen bonding. The β termination is found to contain hydroxyl-hydroxyl hydrogen bonds; the quartz surface hydroxyl hydrogens and oxygens that hydrogen bond with each other exhibit greatly reduced hydrogen bonding to water. Conversely, the hydroxyl hydrogen and oxygens that are not hydrogen bonded to other surface hydroxyls but are connected to those that are show a considerable amount of hydrogen bonding to water. The electron density distribution of an annealed surface of quartz (1010) obtained by XR is in qualitative agreement with electron densities calculated by CMD and AIMD. In all simulation methods, the interfacial water peak appears farther from the surface than observed by XR. Agreement among AIMD, LFF, and XR is observed for the relaxation of the near-surface atoms; however, ClayFF shows a larger discrepancy. Overall, results show that for both terminations of (1010), LFF treats the near-surface structure more accurately whereas ClayFF treats the interfacial water structure more accurately. It is shown that the number of hydroxyl and water hydrogen bonds to the bridging Si-O-Si oxygens connecting the surface silica groups to the rest of the crystal is much greater for the α than the β termination. It is suggested that this may play a role in the greater resistance to dissolution of the β termination than that of the α termination.     

Force Constants and Bond Orders of Nitrogen Bonds

The force constants and the corresponding bond orders of nitrogen bonds have been calculated from the vibrational spectra (infrared and Raman spectra) of a great number of nitrogen compounds. Plotting the maximum bond order of stable nitrogen bonds against the sum of Pauling's electronegativities of the bonding partners (Σx) leads to one continuous curve for the N? X bonds where X represents elements of the first and the second short period of the periodic table. Furthermore, when the bonds formed between these elements are arranged in a coordinate system in such a way that the position of each bond is determined by the difference between the electronegativities of the bonding partners (Δx along the ordinate) and the sum of the electronegativities of the bonding partners (Σx along the abscissa), the bonding partners capable of forming multiple bonds all lie within a closed domain, where their position can be correlated with their polymerizability and other reactivities of the multiple bonds. Also discussed are the orders of bonds between nitrogen and some transition elements. In an appendix, the present methods used to calculate force constants and bond orders are surveyed.     

Chemical bonding in cesium uranyl chloride based on the experimental electron density distribution

Details of the electron density distribution in Cs(2)UO(2)Cl(4) have been obtained from an accurate X-ray diffraction experiment at 20 K. The electron density was described with the Hansen-Coppens multipole model. Topological analysis of the electron density confirms that the U-O bond is probably a triple bond, the U-Cl bonds are incipient covalent interactions, and the Cs-Cl and Cs-O interactions are of the closed-shell type. The results obtained serve as a proof of principle that electron density features related to chemical bonding may be obtained from X-ray data for even the heaviest elements.