Energetics Of Steps Research Articles

Step Structures and Adatom Diffusion on SiC Surfaces

Recent first-principles studies on step structures and adatom diffusion on SiC(0001) surfaces are reviewed. SiC is a promising material for next-generation power electronics, and SiC power devices are already on the market. The obtained formation energies of all the possible atomic steps provide a definite identification of the most relevant atomic step for two vicinal directions inclined toward either <1100> or <1120> direction on SiC(0001) surfaces. Relations between the energetics of surface steps and macroscopic step morphology are discussed. Diffusion mechanism for Si, C, and H adatoms which are three important chemical elements of gas sources of chemical vapor deposition (CVD) for SiC is revealed both on the surface terraces and near the surface steps.

Reconstruction of Thiospinel to Active Sites and Spin Channels for Water Oxidation.

Water electrolysis is a promising technique for carbon neutral hydrogen production. A great challenge remains at developing robust and low-cost anode catalysts. Many pre-catalysts are found to undergo surface reconstruction to give high intrinsic activity in the oxygen evolution reaction (OER). The reconstructed oxyhydroxides on the surface are active species and most of them outperform directly synthesized oxyhydroxides. The reason for the high intrinsic activity remains to be explored. Here, a study is reported to showcase the unique reconstruction behaviors of a pre-catalyst, thiospinel CoFe2 S4 , and its reconstruction chemistry for a high OER activity. The reconstruction of CoFe2 S4 gives a mixture with both Fe-S component and active oxyhydroxide (Co(Fe)Ox Hy ) because Co is more inclined to reconstruct as oxyhydroxide, while the Fe is more stable in Fe-S component in a major form of Fe3 S4 . The interface spin channel is demonstrated in the reconstructed CoFe2 S4 , which optimizes the energetics of OER steps on Co(Fe)Ox Hy species and facilitates the spin sensitive electron transfer to reduce the kinetic barrier of O-O coupling. The advantage is also demonstrated in a membrane electrode assembly (MEA) electrolyzer. This work introduces the feasibility of engineering the reconstruction chemistry of the precatalyst for high performance and durable MEA electrolyzers.

Structurally Precise Two-Transition-Metal Water Oxidation Catalysts: Quantifying Adjacent 3d Metals by Synchrotron X-Radiation Anomalous Dispersion Scattering.

Mixed 3d metal oxides are some of the most promising water oxidation catalysts (WOCs), but it is very difficult to know the locations and percent occupancies of different 3d metals in these heterogeneous catalysts. Without such information, it is hard to quantify catalysis, stability, and other properties of the WOC as a function of the catalyst active site structure. This study combines the site selective synthesis of a homogeneous WOC with two adjacent 3d metals, [Co2Ni2(PW9O34)2]10- (Co2Ni2P2) as a tractable molecular model for CoNi oxide, with the use of multiwavelength synchrotron X-radiation anomalous dispersion scattering (synchrotron XRAS) that quantifies both the location and percent occupancy of Co (∼97% outer-central-belt positions only) and Ni (∼97% inner-central-belt positions only) in Co2Ni2P2. This mixed-3d-metal complex catalyzes water oxidation an order of magnitude faster than its isostructural analogue, [Co4(PW9O34)2]10- (Co4P2). Four independent and complementary lines of evidence confirm that Co2Ni2P2 and Co4P2 are the principal WOCs and that Co2+(aq) is not. Density functional theory (DFT) studies revealed that Co4P2 and Co2Ni2P2 have similar frontier orbitals, while stopped-flow kinetic studies and DFT calculations indicate that water oxidation by both complexes follows analogous multistep mechanisms, including likely Co-OOH formation, with the energetics of most steps being lower for Co2Ni2P2 than for Co4P2. Synchrotron XRAS should be generally applicable to active-site-structure-reactivity studies of multi-metal heterogeneous and homogeneous catalysts.

Electrocatalytic oxidation of ammonia on Pt: Mechanistic insights into the formation of N2 in alkaline media

Electrochemical ammonia oxidation reaction (AOR) is one of the most effective methods to utilize ammonia. Currently, the favorable coupling process during AOR and most important intermediates are still under debate. Herein we used ab initio molecular dynamics (AIMD) method combined with deliberately designed free-energy calculations to thoroughly study the energetics of elementary steps during AOR. The main pathway of N2 formation during AOR is initiated by the dehydrogenation of NH3 to NH2, and subsequent NH2 + NH2 coupling to form N2H4, followed by stepwise dehydrogenation of N2H4 to N2. The Gerischer-Mauerer mechanism was found to be favored in the process. The dehydrogenation of NH3 to NH2 was determined to be the rate-limiting step, and NH2 is the most important intermediate. Through this work, the overall reaction network and corresponding energetics of AOR is revealed, which may enlighten the understanding of AOR and further accelerate corresponding catalyst innovation.

Microscopic Identification of Surface Steps on SiC by Density-Functional Calculations

We have performed density-functional calculations in order to clarify atomic structures and energetics of surface steps on SiC. The obtained energetics of distinct step types on vicinal 3C-SiC(111) surfaces which correspond to 4H- and 6H-SiC(0001) surfaces reveals the atom-scale reason for the experimental observation in the past that the step morphology is straight for the SiC(0001) surfaces inclined toward the 〈1-100〉 direction while it is meandering for the 〈11-20〉 inclined surfaces. The calculations clarify the rebonding between upper- and lower-terrace edge atoms, which is decisive for the energetics of the atomic steps.

Density functional calculations for structures and energetics of atomic steps and their implication for surface morphology on Si-face SiC polar surfaces

We perform large-scale density-functional calculations using the real-space finite-difference scheme endorsed by the Gordon Bell prize in 2011 that reveal detailed atomic and electronic structures of atomic steps on silicon carbide (SiC) polar surfaces for the first time. The accurate structural optimization elucidates characteristic atomic reconstruction among the upper and lower edge atoms, which is peculiar to compound semiconductors having both covalent and ionic nature. The calculated formation energies of all the possible atomic steps lead us to unequivocally identify the abundant atomic steps on the Si-face SiC polar surfaces. The energetics thus obtained for the atomic steps provides a natural and persuasive microscopic reason for the difference in the step morphology observed experimentally, i.e., the meandering and straight step edges depending on the inclined direction on the polar vicinal SiC surfaces. Electron states caused by those atomic steps are also calculated, which assists in the identification of the atomic steps by future experiments.

Energies of Adsorbed Catalytic Intermediates on Transition Metal Surfaces: Calorimetric Measurements and Benchmarks for Theory.

Better catalysts and electrocatalysts are essential for the production and use of clean fuels with less pollution and improved energy efficiency, for making chemicals with less energy and environmental impact, for pollution abatement, and for many other future technologies needed to achieve environmentally friendlier energy supply and chemicals industry. Crucial for rational design of better catalyst and electrocatalyst materials is knowledge of the energies of elementary chemical reactions on late transition metal surfaces. This knowledge would also aid in designing more efficient and stable photocatalysts and batteries for harvesting and storing solar energy. These are all crucial for sustainable living with high quality. Herein, I review measurements of surface reaction energies involving many of the most common adsorbates formed as intermediates on late transition metal surfaces in catalytic and electrocatalytic reactions of interest for energy and environmental technologies. I focus on calorimetric measurements of the heat of molecular and dissociative adsorption of gases on single crystals (i.e., single crystal adsorption calorimetry, or SCAC) that allow the heats of formation of adsorbed intermediates in well-defined structures to be directly determined. Adsorption reactions are often irreversible, and in such cases SCAC is required to get these heats, since the other methods for measuring adsorption energies (equilibrium adsorption isotherms and temperature-programmed desorption) work only for reversible adsorption. Common examples of irreversible adsorption reactions are ones that produce adsorbed molecular fragments or adsorbed molecules such as olefins and aromatic molecules that bind very strongly to non-noble metals. When the heats of formation of different adsorbed molecular fragments are compared to each other, and to their values on different metal surfaces, they reveal which properties of the metal surface and the molecular fragments determine metal-adsorbate bond strengths, and clarify differences in catalytic reactivity between different metals. When combined with earlier adsorption energy measurements, these heats also provide a database of reliable energies of adsorbed catalytic intermediates that serve as crucial benchmarks to guide the development of improved computational methods for calculating the energetics of elementary steps on late transition metal surfaces (i.e., reaction energies and activation barriers), such as density functional theory. The energy accuracy of such computational estimates is crucial for the future of catalysis research and catalyst discovery.

This mechanistic step is “productive”: organic chemistry students' backward-oriented reasoning

If an organic chemistry student explains that she represents a mechanistic step because “it's a productive part of the mechanism,” what meaning could the professor teaching the class attribute to this statement, what is actually communicated, and what does it mean for the student? The professor might think that the explanation is based on knowledge of equilibria of alternative steps. The professor might also assume that the student implies information about how one of the alternatives influences the energetics of subsequent steps or how subsequent steps influence the equilibria of the alternatives. Meanwhile, the student might literally mean that the step is represented simply because it leads to the product. Reasoning about energetic influences has much greater explanatory power than teleological reasoning taking the consequence of mechanistic steps as the reason for their prediction. In both cases, however, the same backward-oriented reasoning is applied. Information about subsequent parts in the mechanism is used to make a decision about prior parts. To qualitatively compare the reasoning patterns and the causality employed by students and expected by their professor, we used a mechanistic approach from philosophy of science that mirrors the directionality of a mechanism and its components: activities, entities, and their properties. Our analysis led to the identification of different reasoning patterns involving backward-oriented reasoning. Participants' use of properties gave additional insight into the students' reasoning and their professor's expectations, which supports the necessity for clear expectations in mechanistic reasoning in organic chemistry classrooms. We present a framework that offers a lens to clarify these expectations and discuss implications of the framework for improving student mechanistic reasoning in organic chemistry.

Repulsive interactions induced by specific adsorption: Anomalous step diffusivity and inadequacy of nearest-neighbor Ising model: (part I experimental)

This is Part I of two closely related papers, where we show that the specific adsorption of anions leads to a failure of the nearest-neighbor Ising model to describe island perimeter curvatures on Au(100) electrodes in dilute KBr, HCl and H2SO4 electrolytes and the therewith derived step diffusivity vs. step orientation. This result has major consequences for theoretical studies aiming at the understanding of growth, diffusion and degradation phenomena. Part I focuses on the experimental data.As shown theoretically in detail in Part II (doi:10.1016/j.susc.2016.03.022), a set of nearest-neighbor and next-nearest-neighbor interaction energies (ϵNN, ϵNNN) can uniquely be derived from the diffusivity of steps along 〈100〉 and 〈110〉. We find strong repulsive next-nearest neighbor (NNN) interaction in KBr and HCl, whereas NNN interaction is negligibly for H2SO4. The NNN repulsive interaction energy ϵNNN therefore correlates positively with the Gibbs adsorption energy of the anions. We find furthermore that ϵNNN increases with increasing Br− and Cl− coverage.The results for ϵNNand ϵNNN are quantitatively consistent with the coverage dependence of the step line tension. We thereby establish a sound experimental base for theoretical studies on the energetics of steps in the presence of specific adsorption.

Controlling catalytic selectivity on metal nanoparticles by direct photoexcitation of adsorbate-metal bonds.

Engineering heterogeneous metal catalysts for high selectivity in thermal driven reactions typically involves the synthesis of nanostructures with well-controlled geometries and compositions. However, inherent relationships between the energetics of elementary steps limit the control of catalytic selectivity through these approaches. Photon excitation of metal catalysts can induce chemical reactivity channels that cannot be accessed using thermal energy, although the potential for targeted activation of adsorbate-metal bonds is limited because the processes of photon absorption and adsorbate-metal bond photoexcitation are typically separated spatially. Here, we show that the use of sub-5-nanometer metal particles as photocatalysts enables direct photoexcitation of hybridized adsorbate-metal states as the dominant mechanism driving photochemistry. Activation of targeted adsorbate-metal bonds through direct photoexcitation of hybridized electronic states enabled selectivity control in preferential CO oxidation in H2 rich streams. This mechanism opens new avenues to drive selective catalytic reactions that cannot be achieved using thermal energy.

Accurate Simulation of Ubiquinone Partition and Diffusion in a Bacterial-Like Membrane Model: Towards Reliable Estimates of the Energetics Involved in the Q-Cycle Mechanism of Cytocrome Bc1

Cytochrome bc1 complex is an ubiquitous component of electron transfer chains in prokariotic and eukariotic organisms. It catalyzes redox reactions of ubiquinone/ubiquinol (UQ) in a pathway called Q-cycle. We are performing computer simulations with molecular mechanical and hybrid quantum mechanical (QM) potentials in order to understand the energetics of several steps involved in this cycle. To start with, we have built and equilibrated a realistic model of a bacterial-like inner membrane, a mixture of phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) 3:1, both with palmitoyiloleoyl chains, using the novel CHARMM36 parameters. We have also parametrized tetraoleoyl cardiolipin (CL) and performed simulations of PE-PC bilayers with 10% CL. We have built a new potential for UQ by improving partial charges and torsional parameters from previously available UQ potentials [1,2]. In comparisons to high-level QM torsional and water or methane interaction profiles, our new UQ potential shows significant improvement over the previous potentials. Thus, we performed potential of mean force calculations with our new UQ potential to obtain the free energy of water/membrane partition of UQ with different isoprenil chain lengths and validated our model by comparison with experimental data [3]. This accurate ubiquinone and bacterial membrane model, is now in use to study the diffusion pathway of UQ through the membrane into Cytochrome bc1 and within its two UQ binding sites.[1] A. Aird et al. Biophysical Journal, 2007, 92(1), 23-33.[2] K. Kaszuba et al. Theor Chem Acc, 2013, 132, 1370-1383.[3] R. Fato et al. Biochemistry, 1996, 35, 2705-2716.

A density functional theory study of atomic steps on stoichiometric rutile TiO2(110)

We present a detailed theoretical study of the energetics of stoichiometric steps on the (110) surface of rutile TiO2. Step structures running along the <001>, <111>, and <110> directions including bulk-terminations and possible reconstructions have been considered. A robust method for extracting surface and step energies of vicinal surfaces, where the surface energies converge slowly with respect to slab thickness, is outlined and used. Based on the calculated step energies a 2D Wulff-construction is presented from which it can be concluded that in equilibrium only oxygen terminated steps running along the <001> directions and reconstructed steps along the <111> directions should be present. Finally it is found that under conditions of stoichiometry the reconstructed <111> steps should be more than twice as abundant as oxygen terminated <001> steps.

Experimental and DFT studies of N 2O decomposition over bare and Co-doped magnesium oxide—insights into the role of active sites topology in dry and wet conditions

Isothermal and TPSR studies of deN 2O reaction were performed over model MgO, and Co–MgO systems. Complementary experiments such as O 2-TPD, H 2O-TPD and IR, supported by DFT molecular modeling were carried out to elucidate the role of topological irregularities such as corners, steps, edges on the principal reaction events in dry and wet environment. The hydroxyl groups produced upon water adsorption were used for selective blocking of the active sites. Topological aspect of the surface reactivity was discussed in terms of the energetics of reaction steps and the relative stability and mobility of reaction intermediates (O 2 2−) and inhibiting (OH − surf) species. Whereas the most active corner sites are depleted by oxygen, produced in the course of N 2O decomposition, the edge and step sites could be eliminated only by more strongly adsorbed water. In steady state conditions the reaction turns over mainly on terrace sites and is moisture insensitive. Upon introduction of Co 2+ ions to magnesium oxide the N 2O conversion curve is shifted by 200 °C towards lower temperatures, due to the change in the N 2O activation step (from anionic redox to cationic redox). However, at such thermal conditions the terrace sites remain still hydroxylated, and the overall reaction rate is clearly deteriorated by water present in the feed.

Kinetic inhibition of calcite (1 0 4) dissolution by aqueous manganese(II)

This study presents evidence of calcite (1 0 4) dissolution inhibition by dissolved manganese(II) through detailed observations of crystal surface morphology. Rates of dissolution have been quantified by direct measurement of surface-normal retreat and etch pit growth at far-from-equilibrium conditions using vertical scanning interferometry. The approach provides new insight into the control that dissolved inorganic carbon (DIC) exerts on manganese inhibition kinetics. Our results show that at 2×10 −6 molal manganese, the rate of overall calcite dissolution is suppressed to close to zero, but only when sufficient CO 3 2− is available in solution. The near arrest of surface-normal dissolution is brought about by the likely reduction in step retreat, inferred through observed variation of etch pit and surface morphology. The inhibition mechanism likely reflects the strong affinity of Mn 2+ for carbonate ion. In solution, this affinity is expressed by formation of a strong complexing ligand (MnCO 3 0). On the (1 0 4) surface, this affinity may govern formation of a similar surface complex that stabilizes reactive sites, thereby inhibiting step movement and defect nucleation. Comparison with results from other metals suggests that inhibition may be understood in the context of the relative energetics of dehydration versus carbonation reaction steps.

Energetics of steps and reconstructed terraces of a two-dimensional semi-infinite solid

Stress and displacement fields of a two-dimensional solid under plane strain are solved subject to surface reconstruction boundary conditions. The alternating lateral Dirac-δ forces at steps owing to the reconstruction obtained by Alerhand et al (1988 Phys. Rev. Lett. 61 1973–6) are recovered from the gradient of the stress field solution. Sinusoidal vertical and lateral displacements on a terrace are obtained, in addition to the vertical force distribution, in the direction normal to the surface. Reconstructed periodic terraces reduce their elastic energy by increasing their average width, but the elastic energy density reaches a finite limit with an increased terrace width. A like-oriented step–step interaction with the force dipole from the surface reconstruction, using the Marchenko–Parshin model, is considered and found to be repulsive. Reconstructed terraces of a vicinal surface are thermodynamically stable when the surface has a large dangling bond energy and a large miscut angle. Small miscut angle or small surface tension tends to destabilize the surface, although our result suggests that a multilayer configuration will metastabilize the terraces owing to the interface elastic mismatch.

Microkinetic Modeling of Ethane Hydrogenolysis on Metals

The microkinetic analysis of ethane hydrogenolysis in the framework of the Sinfelt-Taylor mechanism is carried out using UBI-QEP data on the energetics of elementary steps. On single-crystalline surfaces of Pd(111), Pt(111), and Ni(111), the reaction predominantly occurs via ethyl formation in which the C-C bond is cleaved. The surface concentration of ethylidyne is very low, and ethyl has the highest concentration among all hydrocarbon fragments. For the conditions studied in this work, the activity in ethane hydrogenolysis increases in the series Pd(111) < Pt(111) < Ni(111). According to the results of kinetic modeling, the reaction occurs via quasi-equilibrium steps of adsorption and dissociation of hydrogen and ethane and further, practically irreversible formation of methane.

Nonequilibrium free energy and kinetic roughening of steps on the Kossel(001) surface

This paper studies the nonequilibrium energetics of growth steps. It discusses the energy and free energy of a [100] step on a Kossel(001) crystal surface as a function of the driving force in the case that two-dimensional nucleation is not active. Theoretical expressions for these energies are derived and are found to agree with data obtained from Monte Carlo simulations of step flow. The nonequilibrium expressions allow us to propose that the vanishing of the step free energy beyond a critical value of the driving force defines the onset of the kinetic roughening regime. This is found to agree with the earlier phenomenological criteria for this transition.

Determination of the energetics governing the regulatory step in growth hormone-induced receptor homodimerization

Signaling in the human growth hormone (hGH)-human GH receptor system is initiated by a controlled sequential two-step hormone-induced dimerization of two hGH receptors via their extracellular domains (ECDs). Little is currently known about the energetics governing the important regulatory step in receptor signaling (step 2) because of previously existing experimental barriers in characterizing the binding of the second receptor (ECD2). A further complication is that ECD2 binds through contacts from two spatially distinct sites: through its N-terminal domain to hGH, and to ECD1 through its C-terminal domain, which forms a pseudo-2-fold symmetrical interaction between the stems of the two receptors. We report here a detailed evaluation of the energetics of step 2 binding using a modified surface plasmon resonance method that is able to measure accurately the kinetics of the trimolecular binding process and separate the effects of the two binding sites. The binding kinetics of 23 single and 126 ECD1-ECD2 pair-wise alanine mutations was measured. Although both of the ECD2 binding interfaces were found to be important, the ECD1-ECD2 stem-stem contact is the stronger of the two. It was determined that most residues in the binding interfaces act in additive fashion, and that the six residues common in both ECDs contribute very differently to homodimerization depending on which ECD they reside in. This interface is characterized by a binding "hot-spot" consisting of a core of three residues in ECD1 and two in ECD2. There is no similar hot-spot in the N-terminal domain of ECD2 binding to Site2 of hGH. This study suggests ways to engineer ECD molecules that will bind specifically to either Site1 or Site2 of hGH, providing novel reagents for biophysical and biological studies.

Proton-Coupled Electron Transfer Involving Tyrosine Z in Photosystem II

The O2-evolving complex (OEC) of photosystem II (PSII) catalyzes the oxidation of water to dioxygen. In addition to a tetramanganese-oxo (Mn4) cluster, calcium and chloride ions, the OEC also contains Tyrosine Z (YZ), a redox intermediate in the water oxidation reaction. The redox mechanism employed by YZ is under much debate. Using a novel method to study YZ oxidation based on the kinetic competition with secondary donors, we examine the electron-donation pathways of manganese-depleted PSII over a range of temperature and pH. H/D substitution causes a shift in the onset temperature for YZ oxidation, enabling measurements of lyonium isotope effects. In deuterated samples, the onset temperature for YZ oxidation is upshifted, suggesting that proton movement is a required step. Proton inventory experiments were performed to determine the number of protons that shift during the YZ oxidation reaction. Our findings indicate the movement of a single proton during the rate-limiting step of the oxidation process. The results presented herein demonstrate a need for proton movement in conjunction with YZ oxidation and support previous proposals that a proton-coupled electron transfer (PCET) step is necessary for oxidation of YZ. The possible involvement of PCET in the energetics of specific steps in the mechanism of water oxidation is discussed.

Mechanism and energetics for step merging on a metallic surface captured with scanning tunneling microscopy

Scanning tunneling microscopy has been used to observe oxygen induced microfaceting of Ni(9 7 7) in the temperature range of 390–565 K. Step doubling occurs on this surface provided the step-edges are locally decorated with oxygen. In this letter, time-lapse images of this process have been used to resolve two key steps of the coalescence mechanism. Merging of steps is initiated by the bulging of one step in the downstairs direction towards its neighbor. This rate limiting step is followed by the second mechanistic process, namely zippering of adjacent steps. Merging step contact angles have been analyzed to extract information on the energetics of step–step interactions. These results give a real-space view of the atomic-level surface structural changes which accompany the initial stages of metallic oxidation of interfaces containing extended surface defects.