Bond Breaking Energy Research Articles

Accurate prediction of hydrogen storage capacity of small boron nitride nanocages by dispersion corrected semi-empirical PM6-DH2 method

In this study, we have studied endohedral hydrogen storage capability of several selected BmNm nanocages (m = 12, 24, 36, 48 and 96) and their durability against hydrogen doping by the dispersion corrected semi-empirical PM6-DH2 method. Firstly, we determined performances of the PM6-DH2, PM7, B3LYP methods against the ωB97X-D method, which can make accurate estimations for systems including non-covalent interactions, and found out that PM6-DH2 predicted the stabilities of moderate sized hydrogen doped BN nanocages as accurately as ωB97X-D with computation times of several thousand times faster. Therefore, PM6-DH2 was employed to determine endohedral hydrogen storage capability of BmNm nanocages. It predicted that B24N24, B36N36, B48N48, and B96N96 nanocages have rather significant hydrogen storage percentages of 4.40, 6.67, 8.12 and 12.01%, respectively and B96N96 can endohedrally store up to 142H2 molecules. Analysis of destabilization energies of the complexes encapsulating maximum number of H2 molecules indicated that B24N24 and B48N48 are more durable than B36N36 and B96N96 against hydrogen doping because they can both highly inflate and quite compress hydrogen molecules. In addition, the B–N bond breaking energy for B96N96 is much smaller than the passage barrier of a hydrogen molecule through hexagonal holes, so nanocage breaks instead of hydrogen molecules escaping through the hole. According to all these findings, BN nanocages and larger structures built from them might be considered as good candidates for hydrogen storage.

Multireference second order perturbation theory with a simplified treatment of dynamical correlation.

A multireference second order perturbation theory based on a complete active space configuration interaction (CASCI) function or density matrix renormalized group (DMRG) function has been proposed. This method may be considered as an approximation to the CAS/A approach with the same reference, in which the dynamical correlation is simplified with blocked correlated second order perturbation theory based on the generalized valence bond (GVB) reference (GVB-BCPT2). This method, denoted as CASCI-BCPT2/GVB or DMRG-BCPT2/GVB, is size consistent and has a similar computational cost as the conventional second order perturbation theory (MP2). We have applied it to investigate a number of problems of chemical interest. These problems include bond-breaking potential energy surfaces in four molecules, the spectroscopic constants of six diatomic molecules, the reaction barrier for the automerization of cyclobutadiene, and the energy difference between the monocyclic and bicyclic forms of 2,6-pyridyne. Our test applications demonstrate that CASCI-BCPT2/GVB can provide comparable results with CASPT2 (second order perturbation theory based on the complete active space self-consistent-field wave function) for systems under study. Furthermore, the DMRG-BCPT2/GVB method is applicable to treat strongly correlated systems with large active spaces, which are beyond the capability of CASPT2.

A reaction-controlled diffusion model for the lithiation of silicon in lithium-ion batteries

Silicon is considered as a promising anode material for lithium ion batteries. Despite the great attention on Si anode materials, a consistent description of the diffusion and reaction mechanism at the reaction front of crystalline silicon, amorphous silicon, and delithiated amorphous silicon has not yet been proposed. To better understand those mechanisms, a new reaction-controlled diffusion formulation is proposed. The new formulation makes use of the bond-breaking energy barrier E0 as the key physical quantity. With the consideration of different values of E0, the two-phase diffusion during initial lithiation of both crystalline Si and amorphous Si can be well represented with an evident reaction front. In addition, by varying E0, the one phase lithiation of amorphous Si, obtained after the delithiation process, can be captured with the new formulation. The effect of deformation, hydrostatic pressure at the reaction front, and Li concentration level on the reaction front velocity is taken into account in the proposed model. Numerical simulations are provided to support the model.

Comparative theoretical investigation of the structures, energetics, and stabilities of C7N5H11cages.

Carbon-nitrogen cages are the focus of much research due to their potential use as high energy density materials (HEDMs). Several such cage isomers of C7N5H11, created by modifying the most stable N12 cage, were examined by performing theoretical calculations to evaluate their suitability as potential HEDMs. Calculations were carried out with density functional theory and Møller-Plesset perturbation theory (MP2) using the basis sets 6-31+G(d,p) and cc-pvdz. The relative thermodynamic stabilities of the isomers were explored in two ways: (1) the thermodynamic stability of one isomer was compared to that of another isomer based on their relative energies; (2) the kinetic stabilities of the isomers were determined by calculating the corresponding bond-breaking energies.

Block correlated second order perturbation theory with a generalized valence bond reference function

The block correlated second-order perturbation theory with a generalized valence bond (GVB) reference (GVB-BCPT2) is proposed. In this approach, each geminal in the GVB reference is considered as a "multi-orbital" block (a subset of spin orbitals), and each occupied or virtual spin orbital is also taken as a single block. The zeroth-order Hamiltonian is set to be the summation of the individual Hamiltonians of all blocks (with explicit two-electron operators within each geminal) so that the GVB reference function and all excited configuration functions are its eigenfunctions. The GVB-BCPT2 energy can be directly obtained without iteration, just like the second order Mo̸ller-Plesset perturbation method (MP2), both of which are size consistent. We have applied this GVB-BCPT2 method to investigate the equilibrium distances and spectroscopic constants of 7 diatomic molecules, conformational energy differences of 8 small molecules, and bond-breaking potential energy profiles in 3 systems. GVB-BCPT2 is demonstrated to have noticeably better performance than MP2 for systems with significant multi-reference character, and provide reasonably accurate results for some systems with large active spaces, which are beyond the capability of all CASSCF-based methods.

Imaging bond breaking and vibrational energy transfer in small water containing clusters

This letter presents a brief overview of our recent experimental studies of state-to-state vibrational predissociation (VP) dynamics of small hydrogen bonded (H-bonded) clusters following vibrational excitation. Velocity map imaging (VMI) and resonance-enhanced multiphoton ionization (REMPI) are used to determine accurate bond dissociation energies (D0) of (H2O)2, (H2O)3, HCl–H2O and NH3–H2O. Pair-correlated product energy distributions from the VP of these complexes are also presented and compared to theoretical models. Further insights into mechanisms are obtained from the recent quasi-classical trajectory (QCT) calculations of Bowman and coworkers. The D0 values for (H2O)2 and (H2O)3 are in very good agreement with recent calculated values, and the results are used to estimate the contributions of cooperative interactions to the H-bonding network.

Gas sensitivity of ZnO-based ceramics to vapors of saturated monohydric alcohols

The sensitivity of electrical conductivity of ZnO-based ceramics to vapors of saturated monohydric alcohols was investigated. Its interconnection with physicochemical parameters of alcohols: molecular mass, entropy, Gibbs energy, enthalpy, the bond breaking energy of С–О and О–Н molecular bonds was analyzed.The selectivity of gas-sensitive properties toward vapors of saturated monohydric alcohols, seen in temperature, kinetic and concentration dependences of response was found.A model linking the sensor response, entropy and molecular mass was proposed.

Reduced stress concentration and enhanced fracture toughness by yielding-rehardening combination

A range of tough materials (e.g., metals and polymer solids) exhibit a characteristic mechanical behavior, that is, a combination of yielding and subsequent rehardening. We numerically investigate how the combination of these mechanical behaviors enhances resistance to crack propagation.Our system has a 2-dimensional square lattice structure where pairs of adjacent lattice points are connected by "special" bonds. An isolated bond behaves as a linear spring for small deformations, but yields at a threshold force to produce a plateau in its force-deformation curve, and then shows rehardening on further loading up to a critical force of bond-breaking; on unloading from above the yielding point, the force rapidly decreases with deformation (hysteresis). We simulate crack propagation in the entire system (the square lattice structure) from an initial crack driven by boundary loading. The threshold force for bond-yielding is varied as a simulation parameter, while the critical force for bond-breaking in the rehardening regime is fixed to 1. In other words, the substantial simulation parameter is the ratio between the yielding and breaking forces. We find that the fracture behavior drastically changes depending on the ratio: when the ratio is low, the bond-breaking energy (of a single bond) is low, but more work is required to fracture the entire system via the crack propagation. The opposite tendency between the bond-breaking energy and the fracture work is due to formation of a well-developed yielding zone around the crack tip.

Electrostatically Embedded Many-Body Expansion for Neutral and Charged Metalloenzyme Model Systems

The electrostatically embedded many-body (EE-MB) method has proven accurate for calculating cohesive and conformational energies in clusters, and it has recently been extended to obtain bond dissociation energies for metal-ligand bonds in positively charged inorganic coordination complexes. In the present paper, we present four key guidelines that maximize the accuracy and efficiency of EE-MB calculations for metal centers. Then, following these guidelines, we show that the EE-MB method can also perform well for bond dissociation energies in a variety of neutral and negatively charged inorganic coordination systems representing metalloenzyme active sites, including a model of the catalytic site of the zinc-bearing anthrax toxin lethal factor, a popular target for drug development. In particular, we find that the electrostatically embedded three-body (EE-3B) method is able to reproduce conventionally calculated bond-breaking energies in a series of pentacoordinate and hexacoordinate zinc-containing systems with an average absolute error (averaged over 25 cases) of only 0.98 kcal/mol.

Switchable Conductance in Functionalized Carbon Nanotubes via Reversible Sidewall Bond Cleavage

We propose several covalent functionalizations for carbon nanotubes that display switchable on/off conductance in metallic tubes. The switching action is achieved by reversible control of bond-cleavage chemistry in [1 + 2] cycloadditions via the sp(3) ⇌ sp(2) rehybridization that it induces; this leads to remarkable changes of conductance even at very low degrees of functionalization. Reversible bond-cleavage chemistry is achieved by identifying addends that provide optimal compensation between the bond-preserving through-space π orbital interactions with the tube against the bond-breaking strain energy of the cyclopropane moiety. Several strategies for real-time control, based on redox or hydrolysis reactions, cis-trans isomerization or excited-state proton transfer are proposed. Such designer functional groups would allow for the first time direct control of the electrical properties of metallic carbon nanotubes, with extensive applications in nanoscale devices.

Approaching and Bond Breaking Energies in the C−H Activation and Their Application in Catalyst Design

It was found that the C-H activation barrier can be divided into two parts: C-H approaching and bond breaking energies. The C-H approaching process starts from the reactant and ends at a cross-point structure which is followed by the C-H breaking process. This finding was proved by the intrinsic reaction coordinate (IRC) analysis, vibration frequency (VF) analysis, atom-centered density matrix propagation (ADMP) calculation, and potential energy surface (PES) scan. Further research revealed that the C-H bond breaking energy was related to the electronic structure of the catalyst and the C-H bond dissociation energy of the substrate, whereas the C-H approaching energy was highly relative with the interaction between the substrate and catalyst. These results may be helpful in designing a more effective catalyst.

Assessment and Validation of the Electrostatically Embedded Many-Body Expansion for Metal-Ligand Bonding.

The electrostatically embedded many-body method has been very successful for calculating cohesive energies and relative conformational energies of clusters, and here we extend it to calculate bond breaking energies for metal-ligand bonds in inorganic coordination chemistry. We find that, on average, the electrostatically embedded pairwise additive method is able to predict bond energies yielded by conventional full-system calculations done at the same level of theory to within 2.5 kcal/mol and that the electrostatically embedded three-body method consistently yields energies within 1.0 kcal/mol of the full-system calculations.

A coupled cluster approach with a hybrid treatment of connected triple excitations for bond-breaking potential energy surfaces

An approximate coupled cluster singles, doubles, and triples (CCSDT) method based on the unrestricted Hartree-Fock (UHF) reference, in which the contribution of triple excitations is approximately treated in a hybrid manner [denoted as CCSD(T)-h], is presented. In this approach, canonical UHF molecular orbitals are first transformed into corresponding orbitals so that each alpha-spin orbital is paired with only one beta-spin orbital. Then, active orbitals (occupied or virtual) are automatically selected by setting a threshold for the overlap integrals of corresponding orbitals. With the concept of active orbitals, triple excitations can be divided into two subsets: (1) "active" triples involving at least one occupied active orbital and one virtual active orbital and (2) the remaining triples. The amplitudes of these two classes of triple excitations are obtained via two different approaches. When the present method is employed to study bond-breaking processes, it computationally scales as the seventh power of the system size, because the number of active orbitals involved in such processes is relatively small compared to the total number of the orbitals, and is usually independent on the system size. It has been applied to study the bond-breaking potential energy surfaces in the H(8) model and five small molecules (HF, F(2), CH(4), H(2)O, and N(2)). For all systems under study, the overall performance of CCSD(T)-h is very competitive with that of CCSDT, and much better than that of the UHF-based CCSD(T).

First Principles Studies of Disordered Lithiated Silicon

A protocol to generate disordered structures of lithiated Si was recently developed to reproduce the experimental potential–composition curve of a-Si lithiation at room temperature. In this paper, the bond angle distributions of these structures were studied, showing results consistent with the literature. Charge transfer studies using Bader charge analysis indicate that Li atoms donate 0.7 electrons to Si atoms, as in crystalline phases. The local environments of Si and Li atoms were shown to have a large impact on charge transfer as evaluated by considering neighbors through the effective coordination model. The variation in the effective Li neighbors with composition provides an insight into the cause of the drop in potential, which is observed in the experimental potential–composition curves of a-Si lithiation near . The evolution of the electronic density of states with lithiation was studied, showing behaviors similar to crystalline phases. The limitations of the protocol are discussed in relation to diffusion effects and bond-breaking activation energies. By approximating the lithiation of crystalline Si and the delithiation of as two-phase reactions, calculated potential plateau values were obtained, having a reasonable agreement with experiment .

A DFT study of the effect of K and SiO2 on syngas conversion to methane and methanol over an Mo6P3 cluster

Synthesis gas (CO+H2) conversion to CH4 and CH3OH over an Mo6P3 cluster, an Mo6P3–Si3O9 and a K–Mo6P3–Si3O9 cluster has been studied using density functional theory (DFT). The study focused on the reaction between the intermediate species CH2OHad+Had, comparing methanol formation to C–O bond scission that yields CH2.ad+H2Oad species. The activation energies of both the reactions decreased on the Mo6P3–Si3O9 and the K–Mo6P3–Si3O9 clusters compared to the Mo6P3 cluster. However, on the K–Mo6P3–Si3O9 cluster, the activation energy for methanol formation (12.1 kcal/mol) was higher than the C–O bond-breaking activation energy (9.9 kcal/mol). Although the DFT study predicted preferential formation of CH4 versus CH3OH on all the Mo6P3 clusters, the study also predicted an increased formation of CH3OH with the addition of K and experimental measurements are in agreement with this prediction.

Why Do Cysteine Dioxygenase Enzymes Contain a 3-His Ligand Motif Rather than a 2His/1Asp Motif Like Most Nonheme Dioxygenases?

Density functional theory calculations on the oxygen activation process in cysteine dioxygenase (CDO) and three active site mutants whereby one histidine group is replaced by a carboxylic acid group are reported. The calculations predict an oxygen activation mechanism that starts from an Fe(III)-O-O(*) complex that has close lying singlet, triplet, and quintet spin states. A subsequent spin state crossing to the quintet spin state surfaces leads to formation of a ring-structure whereby an O-S bond is formed. This weakens the central O-O bond, which is subsequently broken to give sulfoxide and an iron-oxo complex. The second oxygen atom is transferred to the substrate after a rotation of the sulfoxide group. A series of calculations were performed on cysteine dioxygenase mutants with a 2His/1Asp motif rather than a 3His motif. These calculations focused on the differences in catalytic and electronic properties of nonheme iron systems with a 3His ligand system versus a 2His/1Asp motif, such as taurine/alpha-ketoglutarate dioxygenase (TauD), and predict why CDO has a 3His ligand system while TauD and other dioxygenases share a 2His/1Asp motif. One mutant (H86D) had the ligand trans to the dioxygen group replaced by acetate, while in another set of calculations the ligand trans to the sulfur group of cysteinate was replaced by acetate (H88D). The calculations show that the ligands influence the spin state ordering of the dioxygen bound complexes considerably and in particular stabilize the quintet spin state more so that the oxygen activation step should encounter a lower energetic cost in the mutants as compared to WT. Despite this, the mutant structures require higher O-O bond breaking energies. Moreover, the mutants create more stable iron-oxo complexes than the WT, but the second oxygen atom transfer to the substrate is accomplished with much higher reaction barriers than the WT system. In particular, a ligand trans to the sulfur atom of cysteine that pushes electrons to the iron will weaken the Fe-S bond and lead to dissociation of this bond in an earlier step in the catalytic cycle than the WT structure. On the other hand, replacement of the ligand trans to the dioxygen moiety has minor effects on cysteinate binding but enhances the barriers for the second oxygen transfer process. These studies have given insight into why cysteine dioxygenase enzymes contain a 3His ligand motif rather than 2His/1Asp and show that the ligand system is essential for optimal dioxygenation activity of the substrate. In particular, CDO mutants with a 2His/1Asp motif may give sulfoxides as byproduct due to incomplete dioxygenation processes.

Simple kinetic Monte Carlo models for dissolution pitting induced by crystal defects

The solid-on-solid kinetic Monte Carlo model of Lasaga and Blum [Geochim. Cosmochim. Acta 50, 2363 (1986)] for dislocation-controlled etch-pit growth has been extended to the growth of etch pits under the control of multiple dislocations and point defects. This required the development of algorithms that are O(10(3))-O(10(4)) times faster than primitive kinetic Monte Carlo models for surfaces with areas in the range of 1024 x 1024-4096 x 4096 lattice sites. Simulations with multiple line defects indicate that the surface morphology coarsens with increasing time and that the coarsening is more pronounced for large bond-breaking activation energies. For small bond breaking activation energies dissolution enhanced by line defects perpendicular to the dissolving surface results in pits with steep sides terminated by deep narrow hollow tubes (nanopipes). Larger bond breaking activation energies lead to shallow pits without deep nanopipes, and if the bond breaking activation energy is large enough, step flow is the primary dissolution mechanism, and pit formation is suppressed. Simplified models that neglect the far field strain energy density but include either a rapidly dissolving core or an initially empty core lead to results that are qualitatively similar to those obtained using models that include the effects of the far field stress and strain. Simulations with a regular array of line defects show that microscopic random thermal fluctuations play an important role in the coarsening process.

BATTLE OF THE ‘FUNCTIONALS’

FOR CHEMISTS, the quick and simple density functional theory (DFT), which readily generates electron structure predictions for ground-state atoms or molecules, seemed to be one of the best computational deals around. DFT predicts electronic properties of atoms or molecules from the densities of their electron clouds, rather than from the solution of the Schrodinger equation for each individual electron’s motion. This greatly simplifies what would otherwise be an intractable, prohibitively expensive computational task. Using not much more than modern desktop computers, chemists routinely include DFT-based predictions in their papers to corroborate their experimental results. But in the past few years, it has become evident that despite its ubiquity, DFT has some serious shortcomings. For example, DFT-calculated C–C bond-breaking energies for larger hydrocarbons are often inaccurate, as are DFT-based reaction-barrier heights. DFT also has trouble describing systems that involve radical cations, charge trans...

Metallic phase formation in oxide films

Metallic particles embedded in the oxide film play an important role in film’s optical property. In this paper it is demonstrated that metallic phases of Ag, Ti, and Pb, can be formed in different oxide films under heating, X-ray photon, and electron radiation. The metallic phase separated from metal oxide film was investigated by X-ray photoelectron spectroscopy technique. Metal oxygen bond breaking and total energy reduction in the film result in the formation of metal in the film. It is necessary to fully understand the formation mechanism of metallic particles so their shapes and distributions can be tailored to achieve the desired film’s properties.

Fragmentation of polyatomic ions produced by electron-loss collisions of butane and isobutane molecules with ions of kiloelectronvolt energy

Fragmentation accompanying the loss of electrons by butane and isobutane (C4H10) molecules in collisions with energy H+, He2+, and Ar6+ ions of kiloelectronvolt energies is studied. The electron density functional technique is applied to C n H2n+2 alkane molecules and their respective C n H 2+2 + ions to carry out quantum-chemical calculations of the atomic spacing, electron total energy for the initial configuration of the ionizing molecules and ions in the ground state, and atomic bond breaking energy necessary to produce different ion fragments. The fragmentation energy is correlated with the fragmentation probability. It is shown that the relative cross sections of ion fragmentation depend primarily on the related energy consumption. However, the process cross section is also strongly affected by the initial configuration of C4H10 isomer molecules, as well as by the amount of dangling and arising atomic bonds involved in the formation of each ion fragment.