Bond-breaking Processes Research Articles

Onset of size independent cationic exchange in nano-sized CoFe2O4 induced by electronic excitation

Present work investigates electronic excitation induced cationic exchange phenomena in nano-sized cobalt ferrites using Mössabaur and X-ray absorption spectroscopies. The electronic excitations were produced by irradiation of 100MeV O+7 at different fluences ranging from 1×1011 to 1×1014ions/cm2. Cubic spinel phase of cobalt ferrite remains preserved after irradiation. However, attributes of crystalline disorder were observed in irradiated materials. Crystallite size remain almost same for pristine and irradiated materials. X-ray absorption fine structure measurements show the preservation of valence state and spin state of metal ions under intense electronic excitation. These measurements also envisage bond breaking process induced by the electronic excitation. Mössbauer spectroscopic measurements also corroborate with the fine structure measurements that the valence state of Fe remains same after irradiation. Paramagnetic doublet which presents in the Mössabaur spectrum of pristine material disappears after irradiation, showing the evolution of irradiation induced magnetic ordering. Fe3+ ion increases with irradiation at octahedral site of spinel lattice. Magnetization of the material slightly increases after irradiation at the fluence of 5×1013 and 1×1014ions/cm2.

Strong Influence of Coadsorbate Interaction on CO Desorption Dynamics on Ru(0001) Probed by Ultrafast X-Ray Spectroscopy and AbInitio Simulations.

We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distribution and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Abinitio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.

Electron transfer mechanisms of DNA repair by photolyase.

Photolyase is a flavin photoenzyme that repairs two DNA base damage products induced by ultraviolet (UV) light: cyclobutane pyrimidine dimers and 6-4 photoproducts. With femtosecond spectroscopy and site-directed mutagenesis, investigators have recently made significant advances in our understanding of UV-damaged DNA repair, and the entire enzymatic dynamics can now be mapped out in real time. For dimer repair, six elementary steps have been characterized, including three electron transfer reactions and two bond-breaking processes, and their reaction times have been determined. A unique electron-tunneling pathway was identified, and the critical residues in modulating the repair function at the active site were determined. The dynamic synergy between the elementary reactions for maintaining high repair efficiency was elucidated, and the biological nature of the flavin active state was uncovered. For 6-4 photoproduct repair, a proton-coupled electron transfer repair mechanism has been revealed. The elucidation of electron transfer mechanisms and two repair photocycles is significant and provides a molecular basis for future practical applications, such as in rational drug design for curing skin cancer.

First-principles study of H2S adsorption and dissociation on Mo(1 1 0)

The dissociative adsorption of H2S on perfect and S-covered Mo(110) surfaces have been studied using density functional theory. Adsorption mechanisms of H2S, SH, S and H on both surfaces were analyzed and all possible potential energy profiles of H2S dissociation processes were mapped out. It indicated that H2S, SH, S, and H energetically favor the short bridge, long bridge, hollow, and hollow sites, respectively, on perfect surface, and favor the top, long bridge, hollow, and hollow sites, respectively, on S-covered surface. The first H2S dehydrogenation on clean surface has a barrier of 0.18–0.31eV, while it required a high energy barrier of 0.40–0.88eV on S-covered surface. The second dehydrogenation showed a lower barrier of 85meV on perfect surface, but a higher barrier of 0.29eV on S-covered surface. All these findings indicated that H2S can easily decompose on perfect Mo(110) surface, but the presence of atomic sulfur went against the H–S bond-breaking process both thermodynamically and kinetically. Finally, densities of electronics states and vibrational frequencies have been used to characterize the interactions between adsorbed species and the substrate.

TiO2 photocatalytic degradation and transformation of oxazaphosphorine drugs in an aqueous environment

This study investigated the TiO2 photocatalytic degradation and transformation of the oxazaphosphorines ifosfamide (IFO), cyclophosphamide (CP) and trofosfamide (TRO). Under the optimum conditions of TiO2=100mg/L, IFO=100μg/L and solution pH=5.5, IFO was completely removed within 10min (k=0.433min−1). The results indicated that OHfree radicals generated by valence holes in the bulk solution were the predominant species for the degradation of IFO. At higher initial concentrations of oxazaphosphorines (20mg/L), >50% of TOC remained after 6h of reaction time, indicating that parent compounds were transformed to byproducts, which exhibit higher Microtox acute toxicities; chlorinated byproducts were likely the source of toxicity. Photocatalytic degradation pathways of the three oxazaphosphorines were proposed. IFO, CP and TRO follow very similar pathways and bond-breaking processes: ketonization and breaking of the CCl bond, the PN bond and the CN bond (N-dechloroethylation). Chloride (Cl−) release is likely the first and primary step in the decomposition process. Several of the identified byproducts were also metabolites, which implies that photocatalytic oxidation proceeds through pathways that are similar to metabolic pathways.

Material modeling for large scale and complex nanostructures: A semi-empirical Hamiltonian method

The advent of the era of nano-structures has also brought about critical issues regarding the determination of stable structures and the associated properties of such systems. From the theoretical perspective, it requires to consider systems of sizes of up to tens of thousands atoms to obtain a realistic picture of thermodynamically stable nano-structure. This is certainly beyond the scope of DFT-based methods. On the other hand, conventional semi-empirical Hamiltonians, which are capable of treating systems of those sizes, do not possess the rigor and accuracy that can lead to a reliable determination of stable structures in nano-systems. During the last dozen years, extensive effort has been devoted to developing methods that can handle systems of nano-sizes on the one hand, while possess first principles-level accuracy on the other. In this review, we present just such a recently developed and well-tested semi-empirical Hamiltonian, referred in the literature as the SCED-LCAO Hamiltonian. Here SCED is the acronym for self-consistent/environment-dependent while LCAO stands for linear combination of atomic orbitals. Compared to existing conventional two-center semiempirical Hamiltonians, the SCED-LCAO Hamiltonian distinguishes itself by remedying the deficiencies of conventional two-center semi-empirical Hamiltonians on two important fronts: the lack of means to determine charge redistribution and the lack of involvement of multi-center interactions. Its framework provides a scheme to self-consistently determine the charge redistribution and includes multi-center interactions. In this way, bond-breaking and bond-forming processes associated with complex structural reconstructions can be described appropriately. With respect to first principles methods, the SCED-LCAO Hamiltonian replaces the time-consuming energy integrations of the self-consistent loop in first principles methods by simple parameterized functions, allowing a speed-up of the self-consistent determination of charge redistribution by two orders of magnitudes. Thus the method based on the SCED-LCAO is no more cumbersome than the conventional semi-empirical methods on the one hand and can achieve the first principle-level accuracy on the other. The parameters and parametric functions for SCED-LCAO Hamiltonian are carefully optimized to model electron-electron correlations and multi-center interactions in an efficient fitting process including a global optimization scheme. To ensure the transferability of the Hamiltonian, the data base chosen in the fitting process contains large amount of physical properties, including (i) the binding energies, the bond lengths, and the symmetries of various clusters covering not only the ground state but also the excited phases, (ii) the binding energies as a function of atomic volume for various crystal phases including also the high pressure phases, and (iii) the electronic band structures of the crystalline systems. In particular, the data bases for excited phases of clusters and high pressure phases in bulk systems are more important when performing molecular dynamics simulations where correct transferable phases are required, such as the excited phases. The validity and the robustness of the SCED-LCAO Hamiltonian have been tested for more complicated Si-, C-, and B-based systems. The success of the SCED-LCAO Hamiltonian will be elucidated through the following applications: (i) the phase transformations of carbon bucky-diamond clusters upon annealing, (ii) the initial stage of growth of single-wall carbon nanotubes (SWCNTs), (iii) the discovery of bulky-diamond SiC clusters, (iv) the morphology and energetics of SiC nanowires (NWs), and (v) the self-assembly of stable SiC based caged nano-structures. A recent upgrade of the SCED-LCAO Hamiltonian, by taking into account the effect on the atomic orbitals due to the atomic aggregation, will also be discussed in this review. This upgrade Hamiltonian has successfully characterized the electron-deficiency in trivalent boron element captured complex chemical bonding in various boron allotropes, which is a big challenge for semi-empirical Hamiltonians.

Copper(II)-mediated transformation of a tridentate non-innocent ligand into a tetradentate salen-type innocent ligand.

A non-innocent ligand, H4L(CH2NH2), was synthesized by introducing a -CH2NH2 group at the ortho carbon atom to the aniline moiety of 2-anilino-4,6-di-tert-butylphenol. The new ligand was characterized by IR and NMR spectroscopy and mass spectrometry techniques. Upon treatment with CuCl2⋅2H2O, this non-innocent ligand provided a mononuclear four-coordinate salen-type Cu(II) complex by complete modification of the ligand backbone. The complex was characterized by IR spectroscopy, mass spectrometry, X-ray single-crystal diffraction, electron paramagnetic resonance (EPR) spectroscopy, and UV/Vis/near-IR spectroscopy techniques. X-ray crystallographic analysis showed an asymmetric environment around the Cu(II) center with a small (≈12°) twist between the two biting planes. Analysis of the X-band EPR spectrum also supported the asymmetric environment and also indicated the presence of an unpaired electron on the dx2-y2 orbital. The UV/Vis/near-IR spectrum showed strong absorption bands for metal-to-ligand charge transfer and ligand-to-metal charge transfer along with a Cu(II) -centered d-d transition. Mechanistic investigation of the formation of complex 1 indicated that modification of the ligand backbone proceeded through ligand-centered amine to imine oxidation as well as through C-N bond-breaking processes. During these processes, 3,5-di-tert-butyl-1,2-benzoquinone and 2-aminobenzylidene were produced. Ammonia, generated in situ through hydrolysis of the imine to the aldehyde, reacted with 3,5-di-tert-butyl-1,2-benzoquinone to form the corresponding 3,5-di-tert-butyl-1,2-iminobenzoquinone moiety, which upon two-electron reduction in the reaction medium formed 3,5-di-tert-butyl-1,2-aminophenol. This aminophenol underwent condensation with the H2L5 ligand that was formed by self-condensation of two molecules of 2-aminobenzaldehyde and provided the modified ligand backbone.

Effects of strain on PdZn(1 0 0) for methoxide decomposition: A DFT study

Density functional theory has been used to systematically investigate the adsorption of methoxide and its decomposed intermediates (i.e. H, O, CH3 and CH2O) as well as methoxide decomposition reaction on strained PdZn(100) surfaces. The reaction and activation energies of methoxide CH and CO bond breaking process showed that expansive strain increased the activity of the PdZn(100) surface toward methoxide decomposition, but reduced its selectivity.

Corrosion in low dielectric constant Si-O based thin films: Buffer concentration effects

Organosilicate glass (OSG) is often used as an interlayer dielectric (ILD) in high performance integrated circuits. OSG is a brittle material and prone to stress-corrosion cracking reminiscent of that observed in bulk glasses. Of particular concern are chemical-mechanical planarization techniques and wet cleans involving solvents commonly encountered in microelectronics fabrication where the organosilicate film is exposed to aqueous environments. Previous work has focused on the effect of pH, surfactant, and peroxide concentration on the subcritical crack growth of these films. However, little or no attention has focused on the effect of the conjugate acid/base concentration in a buffer. Accordingly, this work examines the “strength” of the buffer solution in both acidic and basic environments. The concentration of the buffer components is varied keeping the ratio of acid/base and therefore pH constant. In addition, the pH was varied by altering the acid/base ratio to ascertain any additional effect of pH. Corrosion tests were conducted with double-cantilever beam fracture mechanics specimens and fracture paths were verified with ATR-FTIR. Shifts in the threshold fracture energy, the lowest energy required for bond rupture in the given environment, GTH, were found to shift to lower values as the concentration of the base in the buffer increased. This effect was found to be much larger than the effect of the hydroxide ion concentration in unbuffered solutions. The results are rationalized in terms of the salient chemical bond breaking process occurring at the crack tip and modeled in terms of the chemical potential of the reactive species.

Assessing the accuracy of new geminal-based approaches.

We present a systematic theoretical study on the dissociation of diatomic molecules and their spectroscopic constants using our recently presented geminal-based wave function ansätze. Specifically, the performance of the antisymmetric product of rank two geminals (APr2G), the antisymmetric product of 1-reference-orbital geminals (AP1roG) and its orbital-optimized variant (OO-AP1roG) are assessed against standard quantum chemistry methods. Our study indicates that these new geminal-based approaches provide a cheap, robust, and accurate alternative for the description of bond-breaking processes in closed-shell systems requiring only mean-field-like computational cost. In particular, the spectroscopic constants obtained from OO-AP1roG are in very good agreement with reference theoretical and experimental data.

Significant Quantum Effects in Hydrogen Activation

Dissociation of molecular hydrogen is an important step in a wide variety of chemical, biological, and physical processes. Due to the light mass of hydrogen, it is recognized that quantum effects are often important to its reactivity. However, understanding how quantum effects impact the reactivity of hydrogen is still in its infancy. Here, we examine this issue using a well-defined Pd/Cu(111) alloy that allows the activation of hydrogen and deuterium molecules to be examined at individual Pd atom surface sites over a wide range of temperatures. Experiments comparing the uptake of hydrogen and deuterium as a function of temperature reveal completely different behavior of the two species. The rate of hydrogen activation increases at lower sample temperature, whereas deuterium activation slows as the temperature is lowered. Density functional theory simulations in which quantum nuclear effects are accounted for reveal that tunneling through the dissociation barrier is prevalent for H2 up to ∼190 K and for D2 up to ∼140 K. Kinetic Monte Carlo simulations indicate that the effective barrier to H2 dissociation is so low that hydrogen uptake on the surface is limited merely by thermodynamics, whereas the D2 dissociation process is controlled by kinetics. These data illustrate the complexity and inherent quantum nature of this ubiquitous and seemingly simple chemical process. Examining these effects in other systems with a similar range of approaches may uncover temperature regimes where quantum effects can be harnessed, yielding greater control of bond-breaking processes at surfaces and uncovering useful chemistries such as selective bond activation or isotope separation.

The tensile properties and fracture of the Ni/Cr2O3 interface: First principles simulation

The tensile fracture processes of O-terminated Ni(111)/Cr2O3(0001) interface were investigated using first-principles method. The simulation presents the strain–stress relationship, the Ni deformation and the propagation of crack tip. Atomic configuration and charge density indicate the softer Ni layers deform larger than the harder Cr2O3 layers and that fracture occurs along the metal–oxide interface. The process of bond breaking was also elucidated.

Site-Specific Imaging of Elemental Steps in Dehydration of Diols on TiO2(110)

Scanning tunneling microscopy is employed to follow elemental steps in conversion of ethylene glycol and 1,3-propylene glycol on partially reduced TiO2(110) as a function of temperature. Mechanistic details about the observed processes are corroborated by density functional theory calculations. The use of these two diol reactants allows us to compare and contrast the chemistries of two functionally similar molecules with different steric constraints, thereby allowing us to understand how molecular geometry may influence the observed chemical reactivity. We find that both glycols initially adsorb on Ti sites, where a dynamic equilibrium between molecularly bound and deprotonated species is observed. As the diols start to diffuse along the Ti rows above 230 K, they irreversibly dissociate upon encountering bridging oxygen vacancies. Surprisingly, two dissociation pathways, one via O-H and the other via C-O bond scission, are observed. Theoretical calculations suggest that the differences in the C-O/O-H bond breaking processes are the result of steric factors enforced upon the diols by the second Ti-bound OH group. Above ∼400 K, a new stable intermediate centered on the bridging oxygen (Ob) row is observed. Combined experimental and theoretical evidence shows that this intermediate is most likely a new dioxo species. Further annealing leads to sequential C-Ob bond cleavage and alkene desorption above ∼500 K. Simulations demonstrate that the sequential C-Ob bond breaking process follows a homolytic diradical pathway, with the first C-Ob bond breaking event accompanied with a nonadiabatic electron transfer within the TiO2(110) substrate.

Splitting multiple bonds: A comparison of methodologies on the accuracy of bond dissociation energies

A benchmarking of different quantum chemical methodologies for the splitting of multiply bonded systems is presented, with an emphasis on quantitative reproduction of experimentally determined dissociation energies. New benchmark full configuration interaction (FCI) calculations are presented for nitrogen and acetylene, and comparisons are made between various methods with both the FCI results and with experiment in an effort to understand qualitatively and quantitatively how well these different methods cope with the bond-breaking process. It is found that the multireference methods fare well, but are sometimes slowly convergent with respect to the size of the basis set, and in particular the angular momenta of the polarization functions. Single-reference (SR) wavefunction-based methods perform poorly against full CI, while CCSD(T) is reasonably accurate for comparison with experiment. Density functional theory with hybrid functionals have very quick basis-set convergence, and offer reliable estimates of bond dissociation energies. Spin-restricted SR wavefunctions are found to be poor for such systems, while unrestricted wavefunctions give reasonably good energies, but with severe spin contamination.

Screened environment-dependent reactive empirical bond-order potential for atomistic simulations of carbon materials

A screened environment-dependent reactive empirical bond-order (SED-REBO) potential has been developed for large-scale molecular dynamics (MD) simulations of carbon materials. Based on the second-generation REBO potential developed by Brenner and co-workers [J. Phys.: Condens. Matter 14, 783 (2002)], the SED-REBO potential overcomes the deficiencies of the REBO potential, which arise from a short range of interatomic interactions and their abrupt switching off at the cutoff distance, by increasing the range of interatomic interactions and eliminating the explicit switching function while introducing a simple yet efficient screening function. The increased cutoff distance allows the inclusion of interactions critically important for the physically correct description of bond breaking and bond remaking. An analytic form of the attractive and repulsive pairwise terms was devised to automatically become zero at distances above the cutoff, thus, eliminating the need for the switching function. The screening function effectively screens off the second- and further-nearest-neighbor interactions for calculation of energy and forces in a smooth and continuous way for both compression and expansion. The pairwise attractive and repulsive terms were refitted within a wide range of interatomic distances to properly describe large compressions and expansions of diamond and graphene as well as their behavior near equilibrium. Good performances of the SED-REBO potential to describe bond-breaking processes at extreme tensile stresses are demonstrated in large-scale MD simulations of the nanoindentation of graphene membranes. A computationally efficient version of the SED-REBO potential is introduced for large-scale MD simulations of shock-wave compression in carbon materials. The SED-REBO potential is implemented as a module in the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) and is freely available.

Light-control of liquid crystal alignment from vertical to planar

Continuous or discontinuous transition from vertical to planar alignment was found in nematic cells, containing polyimide alignment layer exposed to linear polarized UV light, depending on whether the alignment layer was mechanically rubbed or not prior the illumination. The polyimide material is designed originally to promote vertical alignment when deposited onto the inner cell substrates' surface. The mechanism behind these observations is complicated. It includes inclination of the alkyl side chains of the polyimide alignment layer towards the rubbing direction and the bond breaking process due to UV illumination which are considered as the key factors for occurrence of such alignment transition.

Orbital Entanglement in Bond-Formation Processes.

The accurate calculation of the (differential) correlation energy is central to the quantum chemical description of bond-formation and bond-dissociation processes. In order to estimate the quality of single- and multireference approaches for this purpose, various diagnostic tools have been developed. In this work, we elaborate on our previous observation [J. Phys. Chem. Lett.2012, 3, 3129] that one- and two-orbital-based entanglement measures provide quantitative means for the assessment and classification of electron correlation effects among molecular orbitals. The dissociation behavior of some prototypical diatomic molecules features all types of correlation effects relevant for chemical bonding. We demonstrate that our entanglement analysis is convenient to dissect these electron correlation effects and to provide a conceptual understanding of bond-forming and bond-breaking processes from the point of view of quantum information theory.

Adhesion: role of bulk viscoelasticity and surface roughness

We study the adhesion between smooth polydimethylsiloxane (PDMS) rubber balls and smooth and rough poly(methyl methacrylate) (PMMA) surfaces, and between smooth silicon nitride balls and smooth PDMS surfaces. From the measured viscoelastic modulus of the PDMS rubber we calculate the viscoelastic contribution to the crack-opening propagation energy γeff(v,T) for a wide range of crack tip velocities v and for several temperatures T. The Johnson–Kendall–Roberts (JKR) contact mechanics theory is used to analyze the ball pull-off force data, and γeff(v,T) is obtained for smooth and rough surfaces. We conclude that γeff(v,T) has contributions of similar magnitude from both the bulk viscoelastic energy dissipation close to the crack tip, and from the bond-breaking process at the crack tip. The pull-off force on the rough surfaces is strongly reduced compared to that of the flat surface, which we attribute mainly to the decrease in the area of contact on the rough surfaces.

Carbon Atoms in Ethanol Do Not Contribute Equally to Formation of Single-Walled Carbon Nanotubes

We propose a unique experimental technique in which isotopically labeled ethanol, e.g., 12CH3-13CH2-OH, is used to trace the carbon atoms during the formation of single-walled carbon nanotubes (SWNTs) by chemical vapor deposition (CVD). The proportion of 13C is determined from Raman spectra of the obtained SWNTs, yielding the respective contribution of ethanol's two different carbon atoms to SWNT formation. Surprisingly, the carbon away from the hydroxyl group is preferably incorporated into the SWNT structure, and this preference is significantly affected by growth temperature, presence of secondary catalyst metal species such as Mo, and even by the substrate material. These experiments provide solid evidence confirming that the active carbon source is not limited to products of gas-phase decomposition such as ethylene and acetylene, but ethanol itself is arriving at and reacting with the metal catalyst particles. Furthermore, even the substrate or other catalytically inactive species directly influences the formation of SWNTs, possibly by changing the local environment around the catalyst or even the reaction pathway of SWNT formation. These unexpected effects, which are inaccessible by conventional techniques, paint a clearer picture regarding the decomposition and bond breaking process of the ethanol precursor during the entire CVD process and how this might influence the quality of the obtained SWNTs.

Rigorously extensive orbital-invariant renormalized perturbative triples corrections from quasi-variational coupled cluster theory

We show that, by making use of the linked tensor objects inherent to the approach, Orbital-optimised Quasi-Variational Coupled Cluster Theory (OQVCCD) leads naturally to a computationally-trivial, rigorously extensive, and orbital-invariant renormalization of the standard (T) correction for the perturbative inclusion of the effects of connected triple excitations. The resulting prototype method, renormalized perturbative triple OQVCCD (R-OQVCCD(T)), is demonstrated to predict potential energy curves for single bond-breaking processes of significantly higher accuracy than OQVCCD with the standard perturbative triple-excitation correction (OQVCCD(T)) itself, and to be in good numerical correspondence with the existing renormalized (R-CCSD(T)) and completely renormalized (CR-CCSD(T)) coupled-cluster singles doubles triples methods, while continuing to provide descriptions of multiple bond-breaking processes of OQVCCD(T) quality.