Dynamic restructuring of supported metal nanoparticles and its implications for structure insensitive catalysis.

Some fundamental concepts of catalysis are not fully explained but are of paramount importance for the development of improved catalysts. An example is the concept of structure insensitive reactions, where surface-normalized activity does not change with catalyst metal particle size. Here we explore this concept and its relation to surface reconstruction on a set of silica-supported Ni metal nanoparticles (mean particle sizes 1-6 nm) by spectroscopically discerning a structure sensitive (CO2 hydrogenation) from a structure insensitive (ethene hydrogenation) reaction. Using state-of-the-art techniques, inter alia in-situ STEM, and quick-X-ray absorption spectroscopy with sub-second time resolution, we have observed particle-size-dependent effects like restructuring which increases with increasing particle size, and faster restructuring for larger particle sizes during ethene hydrogenation while for CO2 no such restructuring effects were observed. Furthermore, a degree of restructuring is irreversible, and we also show that the rate of carbon diffusion on, and into nanoparticles increases with particle size. We finally show that these particle size-dependent effects induced by ethene hydrogenation, can make a structure sensitive reaction (CO2 hydrogenation), structure insensitive. We thus postulate that structure insensitive reactions are actually apparently structure insensitive, which changes our fundamental understanding of the empirical observation of structure insensitivity.

Deactivation Kinetics of Solid Acid Catalyst with Laterally Interacting Protons.

Differences in catalyst deactivation kinetics in solid acid catalysis are studied with catalyst models that allow for lateral interaction between protons. Deactivation of a solid acid catalyst with laterally interacting protons induces inhomogeneity of proton reactivity that develops with time. As a consequence, product selectivity changes and deactivation will accelerate. This is demonstrated by simulations of the deactivation kinetics of the alkylation reaction of propylene with isobutane. The effect of lateral interactions between protons arises because initial catalyst deactivation is not caused by pore blocking or coke deposition but by a molecular mechanism where protons are consumed due to the formation of stable nonreactive carbenium ions. High selectivity to alkylate requires a catalyst with protons of high reactivity. When protons become consumed by formation of stable deactivating carbenium ions, initially reactive protons are converted into protons of lower reactivity. The latter only catalyze deactivating oligomerization reactions. Simulations that compare the deactivation kinetics of a catalyst model with laterally interacting protons and a catalyst model that contains protons of similar but different reactivity, but that do not laterally interact, are compared. These simulations demonstrate that the lateral interaction catalyst model is initially more selective but also has a lower stability. Catalyst deactivation of the alkylation reaction occurs through two reaction channels. One reaction channel is due to oligomerization of reactant propylene. The other deactivation reaction channel is initiated by deprotonation of intermediate carbenium ions that increase alkene concentration. By consecutive reactions, this also leads to deactivation. The hydride transfer reaction competes with oligomerization reactions. It is favored by strongly acid sites that also suppress the deprotonation reaction. Within the laterally interacting proton catalyst model, when reactive protons become deactivated, weakly reactive protons are generated that only catalyze the deactivating alkene oligomerization and consecutive reactions. This rapid formation of the weakly reactive protons is the cause of decreasing selectivity with reaction time and increased rate of deactivation. Solutions of the mean field kinetic equations as well as stochastic simulations are presented. Comparative simulations with a reduced number of neighbors of the protons illustrate decreased deactivation rates when the proton density decreases. Island formation of adsorbed reaction intermediates on the catalyst surface is observed in stochastic kinetics simulations. When alkylation selectivity is high, this island formation increases the rate of catalyst deactivation in comparison to the rate of deactivation according to the mean field studies. A nonlinear dynamics model of proton dynamics is provided, which shows that the differences between stochastic and mean field simulations are due to frustrated proton state percolation.

The challenge of catalyst prediction.

New insights and successful use of computational catalysis are highlighted. This is within the context of remaining issues that prevent theoretical catalysis to be fully predictive of catalyst performance. A major challenge is to include in modelling studies the transient initiation as well as deactivation processes of the catalyst. We will illustrate this using as an example for solid acid catalysis, the alkylation process, and for transition metal catalysis, the Fischer-Tropsch reaction. For the alkylation reaction of isobutane and alkene, an important reaction for high octane gasoline, we will present a deactivation model. For the Fischer-Tropsch reaction, which converts synthesis gas into gasoline grade molecules, we discuss structural reorganization of the catalyst induced by reaction.

Hydride Transfer versus Deprotonation Kinetics in the Isobutane-Propene Alkylation Reaction: A Computational Study.

The alkylation of isobutane with light alkenes plays an essential role in modern petrochemical processes for the production of high-octane gasoline. In this study we have employed periodic DFT calculations combined with microkinetic simulations to investigate the complex reaction mechanism of isobutane-propene alkylation catalyzed by zeolitic solid acids. Particular emphasis was given to addressing the selectivity of the alkylate formation versus alkene formation, which requires a high rate of hydride transfer in comparison to the competitive oligomerization and deprotonation reactions resulting in catalyst deactivation. Our calculations reveal that hydride transfer from isobutane to a carbenium ion occurs via a concerted C-C bond formation between a tert-butyl fragment and an additional olefin, or via deprotonation of the tert-butyl fragment to generate isobutene. A combination of high isobutane concentration and low propene concentration at the reaction center favor the selective alkylation. The key reaction step that has to be suppressed to increase the catalyst lifetime is the deprotonation of carbenium intermediates that are part of the hydride transfer reaction cycle.

Scaling Relations for Acidity and Reactivity of Zeolites.

Zeolites are widely applied as solid acid catalysts in various technological processes. In this work we have computationally investigated how catalytic reactivity scales with acidity for a range of zeolites with different topologies and chemical compositions. We found that straightforward correlations are limited to zeolites with the same topology. The adsorption energies of bases such as carbon monoxide (CO), acetonitrile (CH3CN), ammonia (NH3), trimethylamine (N(CH3)3), and pyridine (C5H5N) give the same trend of acid strength for FAU zeolites with varying composition. Crystal orbital Hamilton populations (COHP) analysis provides a detailed molecular orbital picture of adsorbed base molecules on the Brønsted acid sites (BAS). Bonding is dominated by strong σ donation from guest molecules to the BAS for the adsorbed CO and CH3CN complexes. An electronic descriptor of acid strength is constructed based on the bond order calculations, which is an intrinsic parameter rather than adsorption energy that contains additional contributions due to secondary effects such as van der Waals interactions with the zeolite walls. The bond order parameter derived for the CH3CN adsorption complex represents a useful descriptor for the intrinsic acid strength of FAU zeolites. For FAU zeolites the activation energy for the conversion of π-adsorbed isobutene into alkoxy species correlates well with the acid strength determined by the NH3 adsorption energies. Other zeolites such as MFI and CHA do not follow the scaling relations obtained for FAU; we ascribe this to the different van der Waals interactions and steric effects induced by zeolite framework topology.

Hierarchical control of enzymatic actuators using DNA-based switchable memories.

Inspired by signaling networks in living cells, DNA-based programming aims for the engineering of biochemical networks capable of advanced regulatory and computational functions under controlled cell-free conditions. While regulatory circuits in cells control downstream processes through hierarchical layers of signal processing, coupling of enzymatically driven DNA-based networks to downstream processes has rarely been reported. Here, we expand the scope of molecular programming by engineering hierarchical control of enzymatic actuators using feedback-controlled DNA-circuits capable of advanced regulatory dynamics. We developed a translator module that converts signaling molecules from the upstream network to unique DNA strands driving downstream actuators with minimal retroactivity and support these findings with a detailed computational analysis. We show our modular approach by coupling of a previously engineered switchable memories circuit to downstream actuators based on ß-lactamase and luciferase. To the best of our knowledge, our work demonstrates one of the most advanced DNA-based circuits regarding complexity and versatility.

Particle-based modeling of heterogeneous chemical kinetics including mass transfer.

Connecting the macroscopic world of continuous fields to the microscopic world of discrete molecular events is important for understanding several phenomena occurring at physical boundaries of systems. An important example is heterogeneous catalysis, where reactions take place at active surfaces, but the effective reaction rates are determined by transport limitations in the bulk fluid and reaction limitations on the catalyst surface. In this work we study the macro-micro connection in a model heterogeneous catalytic reactor by means of stochastic rotation dynamics. The model is able to resolve the convective and diffusive interplay between participating species, while including adsorption, desorption, and reaction processes on the catalytic surface. Here we apply the simulation methodology to a simple straight microchannel with a catalytic strip. Dimensionless Damkohler numbers are used to comment on the spatial concentration profiles of reactants and products near the catalyst strip and in the bulk. We end the discussion with an outlook on more complicated geometries and increasingly complex reactions.

Constrained-Orbital Density Functional Theory. Computational Method and Applications to Surface Chemical Processes.

We present a method for performing density-functional theory (DFT) calculations in which one or more Kohn-Sham orbitals are constrained to be localized on individual atoms. This constrained-orbital DFT (CO-DFT) approach can be used to tackle two prevalent shortcomings of DFT: the lack of transparency with regard to the governing electronic structure in large (planewave based) DFT calculations and the limitations of semilocal DFT in describing systems with localized electrons or a large degree of static correlation. CO-DFT helps to address the first of these issues by decomposing complex orbital transformations occurring during elementary chemical processes into simpler and more intuitive transformations. The second issue is addressed by using the CO-DFT method to generate configuration states for multiconfiguration Kohn-Sham calculations. We demonstrate both of these applications for elementary reaction steps involved in the oxygen evolution reaction.

Quantum chemistry of the oxygen evolution reaction on cobalt(ii,iii) oxide - implications for designing the optimal catalyst.

Density functional theory is used to examine the changes in electronic structure that occur during the oxygen evolution reaction (OER) catalyzed by active sites on three different surface terminations of Co3O4. These three active sites have reactive oxo species with differing degrees of coordination by Co cations - a µ(3)-oxo on the (311) surface, a µ(2)-oxo on the (110)-A surface, and an η-oxo on the (110)-B surface. The kinetically relevant step on all surfaces over a wide range of applied potentials is the nucleophilic addition of water to the oxo, which is responsible for formation of the O-O bond. The intrinsic reactivity of a site for this step is found to increase as the coordination of the oxo decreases with the µ(3)-oxo on the (311) surface being the least reactive and the η-oxo on the (110)-B surface being the most reactive. A detailed analysis of the electronic changes occurring during water addition on the three sites reveals that this trend is due to both a decrease in the attractive local Madelung potential on the oxo and a decrease in electron withdrawal from the oxo by Co neighbors. Applying a similar electronic structure analysis to the oxidation steps preceding water addition in the catalytic cycle shows that analogous electronic changes occur during this process, explaining a correlation observed between the oxidation potential of a site and its intrinsic reactivity for water addition. This concept is then used to specify criteria for the design of an optimal OER catalyst at a given applied potential.

Structure Sensitivity of the Oxygen Evolution Reaction Catalyzed by Cobalt(II,III) Oxide.

Quantum chemical calculations and simulated kinetics were used to examine the structure sensitivity of the oxygen evolution reaction on several surface terminations of Co3O4. Active sites consisting of two adjacent Co(IV) cations connected by bridging oxos were identified on both the (001) and (311) surfaces. Formation of the O-O bond proceeds on these sites by nucleophilic attack of water on a bridging oxo. It was found that the relative turnover frequencies for the different sites are highly dependent on the overpotential, with the dual-Co site on the (311) surface being most active at medium overpotentials (0.46-0.77 V), where O-O bond formation by water addition is rate limiting. A similar dual-Co site on the (001) surface is most active at low overpotentials (<0.46 V), where O2 release is rate limiting, and a single-Co site on the (110) surface is most active at overpotentials that are high enough (>0.77 V) to form a significant concentration of highly reactive terminal Co(V)═O species. Two overpotential-dependent Sabatier relationships were identified based on the Brønsted basicity and redox potential of the active site, explaining the change in the active site with overpotential. The (311) dual-Co site that is most active in the medium overpotential range is consistent with recent experimental observations suggesting that a defect site is responsible for the observed oxygen evolution activity and that a modest concentration of superoxo intermediates is present on the surface. Importantly, we find that it is essential to consider the kinetics of the water addition and O2 release steps rather than only the thermodynamics.

The role of a structure directing agent tetramethylammonium template in the initial steps of silicate oligomerization in aqueous solution.

The understanding of the formation of silicate oligomers in the initial stage of zeolite synthesis is of fundamental scientific and technological importance. The use of different organic structure directing agents is known to be a key factor in the formation of different silicate species, and the final zeolite structure. Tetramethylammonium (TMA(+)), for example, is indispensable for the formation of the LTA zeolite type. However, the role of a TMA(+) template has not yet been elucidated at the molecular level. In this study, ab initio molecular dynamic simulations were combined with thermodynamic integration to arrive at an understanding of the role of TMA(+) in the formation of various silicate species, ranging from dimer to 4-ring. Free energy profiles show that trimer and 3-ring silicate are less favourable than other oligomers such as linear tetramer, branched tetramer and 4-ring structures. TMA(+) exhibits an important role in controlling the predominant species in solution via its coordination with silicate structures during the reaction process. This can explain that formation of D4R·8TMA crystals, as observed in experiment, is controlled by the single 4-ring formation step.

Synergy between TiO2 and Co(x)O(y) sites in electrocatalytic water decomposition.

A computational study of the cooperative effect of a small four-atom Co oxide cluster supported on the TiO2 anatase (100) surface in the electrochemical water splitting reaction is presented. The results have been obtained including explicit solvent water molecules by means of Car-Parrinello MD simulations. Reaction steps in the catalytic cycle determined involve the formation of TiO2 surface hydroxyl groups as well as elementary reaction steps on the Co oxide cluster. Essential is the observation of O-O bond formation at the inter-phase of Co oxide particles and the TiO2 support.

The optimally performing Fischer-Tropsch catalyst.

Microkinetics simulations are presented based on DFT-determined elementary reaction steps of the Fischer-Tropsch (FT) reaction. The formation of long-chain hydrocarbons occurs on stepped Ru surfaces with CH as the inserting monomer, whereas planar Ru only produces methane because of slow CO activation. By varying the metal-carbon and metal-oxygen interaction energy, three reactivity regimes are identified with rates being controlled by CO dissociation, chain-growth termination, or water removal. Predicted surface coverages are dominated by CO, C, or O, respectively. Optimum FT performance occurs at the interphase of the regimes of limited CO dissociation and chain-growth termination. Current FT catalysts are suboptimal, as they are limited by CO activation and/or O removal.

Correlating Fischer-Tropsch activity to Ru nanoparticle surface structure as probed by high-energy X-ray diffraction.

Synchrotron X-ray diffraction coupled to atomic pair distribution function analysis and Reverse Monte Carlo simulations is used to determine the atomic-scale structure of Ru nanoparticle catalysts for the Fischer-Tropsch reaction. The rate of CO hydrogenation strongly correlates with the abundance of surface atoms with coordination numbers of 10 and 11. DFT calculations confirm that CO dissociation proceeds with a low barrier on these Ru surface atom ensembles.

DFT simulations of water adsorption and activation on low-index α-Ga2O3 surfaces.

Density functional theory (DFT) calculations are used to explore water adsorption and activation on different α-Ga2O3 surfaces, namely (001), (100), (110), and (012). The geometries and binding energies of molecular and dissociative adsorption are studied as a function of coverage. The simulations reveal that dissociative water adsorption on all the studied low-index surfaces are thermodynamically favorable. Analysis of surface energies suggests that the most preferentially exposed surface is (012). The contribution of surface relaxation to the respective surface energies is significant. Calculations of electron local density of states indicate that the electron-energy band gaps for the four investigated surfaces appears to be less related to the difference in coordinative unsaturation of the surface atoms, but rather to changes in the ionicity of the surface chemical bonds. The electrochemical computation is used to investigate the hydrogen evolution reaction (HER) and the oxygen evolution reaction (OER) on α-Ga2O3 surfaces. Our results indicate that the (100) and (110) surfaces, which have low stability, are the most favorable ones for HER and OER, respectively.

Molecular simulation of protein encapsulation in vesicle formation.

Liposomes composed of fatty acids and phospholipids are frequently used as model systems for biological cell membranes. In many applications, the encapsulation of proteins and other biomacromolecules in these liposomes is essential. Intriguingly, the concentration of entrapped material often deviates from that in the solution where the liposomes were formed. While some reports mention reduced concentrations inside the vesicles, concentrations are also reported to be enhanced in other cases. To elucidate possible drivers for efficient encapsulation, we here investigate the encapsulation of model proteins in spontaneously forming vesicles using molecular dynamics simulations with a coarse grained force field for fatty acids and phospholipids as well as water-soluble and transmembrane proteins. We show that, in this model system, the encapsulation efficiency is dominated by the interaction of the proteins with the membrane, while no significant dependence is observed on the size of the encapsulated proteins nor on the speed of the vesicle formation, whether reduced by incorporation of stiff transmembrane proteins or by the blocking of the bilayer bulging by the presence of another membrane.

Microkinetics of oxygenate formation in the Fischer-Tropsch reaction.

Microkinetics simulations are presented on the intrinsic activity and selectivity of the Fischer-Tropsch reaction with respect to the formation of long chain oxygenated hydrocarbons. Two different chain growth mechanisms are compared: the carbide chain growth mechanism and the CO insertion chain growth mechanism. The microkinetics simulations are based on quantum-chemical data on reaction rate parameters of the elementary reaction steps of the Fischer-Tropsch reaction available in the literature. Because the overall rate constant of chain growth remains too low the CO insertion chain growth mechanism is not found to produce higher hydrocarbons, except for ethylene and acetaldehyde or the corresponding hydrogenated products. According to the carbide mechanism available quantum-chemical data are consistent with high selectivity to long chain oxygenated hydrocarbon production at low temperature. The anomalous initial increase with temperature of the chain growth parameter observed under such conditions is reproduced. It arises from the competition between the apparent rate of C-O bond activation to produce "CHx" monomers to be inserted into the growing hydrocarbon chain and the rate of chain growth termination. The microkinetics simulations data enable analysis of selectivity changes as a function of critical elementary reaction rates such as the rate of activation of the C-O bond of CO, the insertion rate of CO into the growing hydrocarbon chain or the rate constant of methane formation. Simulations show that changes in catalyst site reactivity affect elementary reaction steps differently. This has opposing consequences for oxygenate production selectivity, so an optimizing compromise has to be found. The simulation results are found to be consistent with most experimental data available today. It is concluded that Fischer-Tropsch type catalysis has limited scope to produce long chain oxygenates with high yield, but there is an opportunity to improve the yield of C2 oxygenates.

Catalyst nano-particle size dependence of the Fischer-Tropsch reaction.

Computational catalytic studies indicate that the elementary reactions that constitute the Fischer-Tropsch reaction strongly dependent on the structure of the catalyst reaction center. Recent experimental evidence is available that, for metallic Fischer-Tropsch catalysts such as Co or Ru, the very small metallic particles show altered catalytic performance. To distinguish between changes in the relative concentration of reaction centres, changes in chemical reactivity, or rate controlling steps, transient SSITKA data are extremely useful. Here, we present kinetics simulations to extract molecular kinetic information from SSITKA data. We have applied such simulations to interpret published experimental SSITKA data on nano-particle size dependent Fischer-Tropsch (FT) kinetics. The FT catalytic cycle consists of four essential reaction steps. Their relative size determines activity as well as selectivity. The simulated SSITKA indicate three different regimes with different kinetic behaviour, where the two fundamental regimes to distinguish are the monomer-formation-limited and the chain-growth-limited regime. Particle size changes shift kinetics from one to the other regime. We note different effects of supports and choice of metal composition on changes in elementary rates or the relative number of reactive centres when the particle size is decreased in the nanometre regime.

Roughening of Pt nanoparticles induced by surface-oxide formation.

Using density functional theory (DFT) and thermodynamic considerations we studied the equilibrium shape of Pt nanoparticles (NPs) under electrochemical conditions. We found that at very high oxygen coverage, obtained at high electrode potentials, the experimentally-observed tetrahexahedral (THH) NPs consist of high-index (520) faces. Since high-index surfaces often show higher (electro-)chemical activity in comparison to their close-packed counterparts, the THH NPs can be promising candidates for various (electro-)catalytic applications.