Understanding the physics and chemistry of reaction mechanisms from atomic contributions: a reaction force perspective

Studying chemical reactions involves the knowledge of the reaction mechanism. Despite activation barriers describing the kinetics or reaction energies reflecting thermodynamic aspects, identifying the underlying physics and chemistry along the reaction path contributes essentially to the overall understanding of reaction mechanisms, especially for catalysis. In the past years the reaction force has evolved as a valuable tool to discern between structural changes and electrons' rearrangement in chemical reactions. It provides a framework to analyze chemical reactions and additionally a rational partition of activation and reaction energies. Here, we propose to separate these energies further in atomic contributions, which will shed new insights in the underlying reaction mechanism. As first case studies we analyze two intramolecular proton transfer reactions. Despite the atom based separation of activation barriers and reaction energies, we also assign the participation of each atom in structural changes or electrons' rearrangement along the intrinsic reaction coordinate. These participations allow us to identify the role of each atom in the two reactions and therfore the underlying chemistry. The knowledge of the reaction chemistry immediately leads us to suggest replacements with other atom types that would facilitate certain processes in the reaction. The characterization of the contribution of each atom to the reaction energetics, additionally, identifies the reactive center of a molecular system that unites the main atoms contributing to the potential energy change along the reaction path.     

Insights in the plasma-assisted growth of carbon nanotubes through atomic scale simulations: effect of electric field

Carbon nanotubes (CNTs) are nowadays routinely grown in a thermal CVD setup. State-of-the-art plasma-enhanced CVD (PECVD) growth, however, offers advantages over thermal CVD. A lower growth temperature and the growth of aligned freestanding single-walled CNTs (SWNTs) makes the technique very attractive. The atomic scale growth mechanisms of PECVD CNT growth, however, remain currently entirely unexplored. In this contribution, we employed molecular dynamics simulations to focus on the effect of applying an electric field on the SWNT growth process, as one of the effects coming into play in PECVD. Using sufficiently strong fields results in (a) alignment of the growing SWNTs, (b) a better ordering of the carbon network, and (c) a higher growth rate relative to thermal growth rate. We suggest that these effects are due to the small charge transfer occurring in the Ni/C system. These simulations constitute the first study of PECVD growth of SWNTs on the atomic level.     

Molecular scale simulations on thermoset polymers: A review

This article reviews the field of molecular simulations of thermoset polymers. This class of polymers is of interest in applications ranging from structural components for aerospace to electronics packaging and predictive simulations of their response is playing an increasing role in understanding the molecular origin of their properties and complementing experiments in the search for tailored materials for specific applications. It focuses on modeling and simulation of the process of curing to predict the molecular structure of these polymers and their thermomechanical response by all-atom molecular dynamics simulations. Results from Monte Carlo and coarse-grained simulations are briefly summarized. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 103–122     

Heterogeneous catalysis on the atomic scale

Information about the elementary processes underlying heterogeneous catalysis may be obtained by investigating well-defined single crystal surfaces. The success of this "surface science" approach for "'real" catalysis can be demonstrated, for example, with ammonia synthesis. The progress of catalytic reactions can be observed on an atomic scale by applying scanning tunneling microscopy and other surface physical techniques, as is shown with different examples in this paper: CO oxidation on a Pt(111) surface proceeds preferentially along the boundaries between adsorbed O and CO patches. Ru is practically inactive for the same reaction under lower pressure conditions but is transformed into RuO2 under atmospheric pressure conditions, where part of the surface Ru atoms function as coordinatively unsaturated sites (cus). In contrast, in the hydrogen oxidation reaction on Pt(111), an autocatalytic reaction step comes into prominence, and is responsible for the formation of propagating concentration patterns on the surface as a characteristic of nonlinear dynamics. Additionally, the limits of the concept of thermal equilibrium in surface rate processes are explored by applying ultrafast (femtosecond) laser techniques.     

The Heck-Mizoroki cross-coupling reaction: a mechanistic perspective

The Heck-Mizoroki cross-coupling reaction is an important part of the synthetic chemist's toolbox, and it has been applied to a huge variety of different substrates. In contrast, the mechanism of the process is much less studied, and consequently less understood. There have been numerous studies reported over recent years, both experimental and theoretical, aimed at uncovering the inner working of this palladium-mediated coupling process. This perspective aims to review and compare these works and to provide an up-to-date view of this reaction.     

A new scale of atomic electronegativities

A new formula for the calculation of atomic electronegativities from the atomic size and nuclear effective charge is proposed. The formula has the same dimensionality as the one used for the thermochemical scale. The calculated ionic and van der Waals atomic electronegativities are used for the interpretation of the bond nature in binary and coordination compounds (in particular, the bond ionicity is calculated in molecules and crystals of the AB type).Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 1, pp. 32–37, January, 1993.     

The structure of poly(carbonsuboxide) on the atomic scale: a solid-state NMR study

In this contribution we present a study of the structure of amorphous poly(carbonsuboxide) (C3O2)x by 13C solid-state NMR spectroscopy supported by infrared spectroscopy and chemical analysis. Poly(carbonsuboxide) was obtained by polymerization of carbonsuboxide C3O2, which in turn was synthesized from malonic acid bis(trimethylsilylester). Two different 13C labeling schemes were applied to probe inter- and intramonomeric bonds in the polymer by dipolar solid-state NMR methods and also to allow quantitative 13C MAS NMR spectra. Four types of carbon environments can be distinguished in the NMR spectra. Double-quantum and triple-quantum 2D correlation experiments were used to assign the observed peaks using the through-space and through-bond dipolar coupling. In order to obtain distance constraints for the intermonomeric bonds, double-quantum constant-time experiments were performed. In these experiments an additional filter step was applied to suppress contributions from not directly bonded 13C,13C spin pairs. The 13C NMR intensities, chemical shifts, connectivities and distances gave constraints for both the polymerization mechanism and the short-range order of the polymer. The experimental results were complemented by bond lengths predicted by density functional theory methods for several previously suggested models. Based on the presented evidence we can unambiguously exclude models based on gamma-pyronic units and support models based on alpha-pyronic units. The possibility of planar ladder- and bracelet-like alpha-pyronic structures is discussed.     

Plasma density effects on atomic reaction rates

Plasma modeling and diagnostics commonly involve solution of rate equations for the population densities of impurity ions in their excited and charge states. Construction of the rate equations requires a complete set of atomic transition rates for all the charge and excited states involved. However, the rates are themselves affected by the host plasma ions and electrons. The ionic and electronic effects in a two-component plasma are intimately interconnected, especially when the rate equations are simplified for computational purpose in the determination of ionization balance. We formulate a coherent approach to the problem of the plasma density effect, and apply it to carbon impurities in a hydrogen plasma. Both the plasma field distortion of atomic states and the corresponding rates by the plasma ions and stochastic plasma collisional transitions caused by the plasma electrons are included. The latter effect is estimated by constructing an effective collisional transition operator, and the electron-ion recombination processes are explicitly evaluated. It is shown that, these two effects of the ionic field distortions and electronic collisions tend to cancel each other, resulting in many cases in reducing the overall effect of the plasma density on the ionization.     

Oxygen evolution on electrodes of different roughness: an electrochemical noise study

Rough and porous Ni layers have been obtained by cathodic deposition from a NiCl₂, NH₄Cl solution, at high current density. Characterisation by SEM has shown that they consisted of micro-dendrites separated by pores with a typical diameter of 1 m. In addition, circular hollows (10–100 m in diameter) were found on the deposit surface; their density varied with the deposition current density and deposition charge. The surface roughness of the Ni deposits, measured by EIS, was found to increase roughly linearly with the deposition charge, and to be little dependent on current density, provided a threshold value was exceeded. The oxygen evolution reaction has been studied on these electrodes by simultaneous real-time measurements of potential and electrolyte resistance fluctuations. The analysis of the electrochemical noise indicated that the dimensions of oxygen bubbles detaching from the electrodes slightly increased with the deposit surface roughness. It is not clear, however, whether or not this increase was associated with the effect of the small (1 m) or the large (10–100 m) features on the electrode-bubble interactions.     

Electrophoretically mediated reaction of glycosidases at a nanoliter scale

We have investigated electrophoretically mediated microanalysis (EMMA) for the assay of a native glyco-enzyme. As a representative of this class of enzyme, beta-glucosidase was selected, and the reaction was analyzed. Our EMMA was based on the plug-plug interaction of enzyme and substrate plugs, which is essential to reduce quantities of materials. Furthermore, we have addressed the problem of incompatibility of the enzymatic reaction and separation of the reactants. As a result, EMMA of native glycosidase was achieved with a reaction volume of approximately 20 nL and the Michaelis constant was estimated according to the Lineweaver-Burk plot. The current method may have advantages over traditional assay methods, especially in terms of the amount of enzyme (ng order) and substrate (pmol order) required for a reaction.     

Transition metal-catalysed intermolecular reaction of allenes with oxygen nucleophiles: a perspective

Transition metal catalysed hydroalkoxylation of allenes has received much attention in recent years, and both the intra- and intermolecular versions have been reported. Gold(I) complexes are among the most active catalysts for these processes. This critical perspective article will cover the progress in this field, analysing the intermolecular metal-catalysed reaction of allenes using palladium, iridium, rhodium, ruthenium, gold and platinum, in the presence of alcohols, water or carboxylic acids, and the mechanistic implications of these processes depending on the metal used.     

Efficient stochastic simulations of complex reaction networks on surfaces

Surfaces serve as highly efficient catalysts for a vast variety of chemical reactions. Typically, such surface reactions involve billions of molecules which diffuse and react over macroscopic areas. Therefore, stochastic fluctuations are negligible and the reaction rates can be evaluated using rate equations, which are based on the mean-field approximation. However, in case that the surface is partitioned into a large number of disconnected microscopic domains, the number of reactants in each domain becomes small and it strongly fluctuates. This is, in fact, the situation in the interstellar medium, where some crucial reactions take place on the surfaces of microscopic dust grains. In this case rate equations fail and the simulation of surface reactions requires stochastic methods such as the master equation. However, in the case of complex reaction networks, the master equation becomes infeasible because the number of equations proliferates exponentially. To solve this problem, we introduce a stochastic method based on moment equations. In this method the number of equations is dramatically reduced to just one equation for each reactive species and one equation for each reaction. Moreover, the equations can be easily constructed using a diagrammatic approach. We demonstrate the method for a set of astrophysically relevant networks of increasing complexity. It is expected to be applicable in many other contexts in which problems that exhibit analogous structure appear, such as surface catalysis in nanoscale systems, aerosol chemistry in stratospheric clouds, and genetic networks in cells.     

原子的边界半径

本文建议和讨论2了原子大小的一种新量度-原子的边界半径, 经出了边界半径的周期表。对于惰性气体原子和汞原子, 有实验测得的有效半径, 它们与边界半径符合得相当好。原子的边界半径与实验的van der Waals半径有良好的线性关系。因此, 由边界半径可以预言某些原子的有效半径以及van der Waals半径。     

Mechanisms of heterogeneous crystal growth in atomic systems: insights from computer simulations

In this paper we analyze the atomic-level structure of solid/liquid interfaces of Lennard-Jones fcc systems. The 001, 011, and 111 faces are examined during steady-state growth and melting of these crystals. The mechanisms of crystallization and melting are explored using averaged configurations generated during these steady-state runs, where subsequent tagging and labeling of particles at the interface provide many insights into the detailed atomic behavior at the freezing and melting interfaces. The interfaces are generally found to be rough and we observe the structure of freezing and melting interfaces to be very similar. Large structural fluctuations with solidlike and liquidlike characteristics are apparent in both the freezing and melting interfaces. The behavior at the interface observed under either growth or melting conditions reflects a competition between ordering and disordering processes. In addition, we observe atom hopping that imparts liquidlike characteristics to the solid side of the interfaces for all three crystal faces. Solid order is observed to extend as rough, three-dimensional protuberances through the interface, particularly for the 001 and 011 faces. We are also able to reconcile our different measures for the interfacial width and address the onset of asymmetry in the growth rates at high rates of crystal growth/melting.     

Oxygen evolution on La0.5Ba0.5CoO3: Transient measurements

The recovery behavior of an aged La_0.5Ba_0.5CoO₃ electrode after interrupting a cathodic discharge current (forced decay, all starting from a high prepolarized state) at a still positive overpotential of 150 mV is discussed. It was found that the potential rises again after interrupting the cathodic current. This rise in potential decreases with decreasing cathodic currents when the electrodes are stabilized at the same starting overpotential before applying the cathodic current. The rise in potential also decreases with decreasing starting overpotential for the same cathodic discharge current. From these measurements it was concluded that higher oxides are present to a certain depth in the oxide layer at high positive overpotentials.Open-circuit decay measurements with different starting overpotentials were performed, all showing logarithmic slopes of ～ 50 mV/dec. The decay rates increased for lower starying overpotentials. Impedances were measured during a decay, from which effective capacitances were calculated. For a given overpotential, the capacitances during a decay were practically constant in the overpotential range from 220 to 150 mV for a given staring overpontential. But for higher starting overpotentials the capacitances were found to be higher. These effects are explained by a change in effective surface area for different starting overpotentials caused by the above-mentioned higher oxides blocking the surface.