Evaluation of Sampling Algorithms Used for Bayesian Uncertainty Quantification of Molecular Dynamics Force Fields.

New Bayesian parameter estimation methods have the capability to enable more physically realistic and reliable molecular dynamics (MD) simulations by providing accurate estimates of uncertainties of force-field (FF) parameters and associated properties. However, the choice of which Bayesian parameter estimation algorithm to use has not been widely investigated, despite its impact on the effective exploration of parameter space. Here, using a case example of the Embedded Atom Method (EAM) FF parameters, we investigated the ramifications of several of the algorithm choices. We found that Ensemble Slice Sampling (ESS) and Affine-Invariant Ensemble Sampling (AIES) demonstrate a new level of superior performance, culminating in more accurate parameter and property estimations with tighter uncertainty bounds, compared to traditional methods such as Metropolis-Hastings (MH), Gradient Search (GS), and Uniform Random Sampler (URS). We demonstrate that Bayesian Uncertainty Quantification with ESS and AIES leads to significantly more accurate and reliable predictions of the FF parameters and properties. The results suggest that ESS and AIES should be used to obtain more accurate parameter and uncertainty estimations while providing deeper physical insights.

Toward Quantum Chemical Free Energy Simulations of Platinum Nanoparticles on Titania Support.

Platinum nanoparticles (Pt-NPs) supported on titania surfaces are costly but indispensable heterogeneous catalysts because of their highly effective and selective catalytic properties. Therefore, it is vital to understand their physicochemical processes during catalysis to optimize their use and to further develop better catalysts. However, simulating these dynamic processes is challenging due to the need for a reliable quantum chemical method to describe chemical bond breaking and bond formation during the processes but, at the same time, fast enough to sample a large number of configurations required to compute the corresponding free energy surfaces. Density functional theory (DFT) is often used to explore Pt-NPs; nonetheless, it is usually limited to some minimum-energy reaction pathways on static potential energy surfaces because of its high computational cost. We report here a combination of the density functional tight binding (DFTB) method as a fast but reliable approximation to DFT, the steered molecular dynamics (SMD) technique, and the Jarzynski equality to construct free energy surfaces of the temperature-dependent diffusion and growth of platinum particles on a titania surface. In particular, we present the parametrization for Pt-X (X = Pt, Ti, or O) interactions in the framework of the second-order DFTB method, using a previous parametrization for titania as a basis. The optimized parameter set was used to simulate the surface diffusion of a single platinum atom (Pt1) and the growth of Pt6 from Pt5 and Pt1 on the rutile (110) surface at three different temperatures (T = 400, 600, 800 K). The free energy profile was constructed by using over a hundred SMD trajectories for each process. We found that increasing the temperature has a minimal effect on the formation free energy; nevertheless, it significantly reduces the free energy barrier of Pt atom migration on the TiO2 surface and the transition state (TS) of its deposition. In a concluding remark, the methodology opens the pathway to quantum chemical free energy simulations of Pt-NPs' temperature-dependent growth and other transformation processes on the titania support.

Design of tough adhesive from commodity thermoplastics through dynamic crosslinking.

Tough adhesives provide resistance against high debonding forces, and these adhesives are difficult to design because of the simultaneous requirement of strength and ductility. Here, we report a design of tough reversible/recyclable adhesive materials enabled by incorporating dynamic covalent bonds of boronic ester into commodity triblock thermoplastic elastomers that reversibly bind with various fillers and substrates. The spectroscopic measurements and density functional theory calculations unveil versatile dynamic covalent binding of boronic ester with various hydroxy-terminated surfaces such as silica nanoparticles, aluminum, steel, and glass. The designed multiphase material exhibits exceptionally high adhesion strength and work of debonding with a rebonding capability, as well as outstanding mechanical, thermal, and chemical resistance properties. Bonding and debonding at the interfaces dictate hybrid material properties, and this revelation of tailored dynamic interactions with multiple interfaces will open up a new design of adhesives and hybrid materials.

Harnessing strong metal-support interactions via a reverse route.

Engineering strong metal-support interactions (SMSI) is an effective strategy for tuning structures and performances of supported metal catalysts but induces poor exposure of active sites. Here, we demonstrate a strong metal-support interaction via a reverse route (SMSIR) by starting from the final morphology of SMSI (fully-encapsulated core-shell structure) to obtain the intermediate state with desirable exposure of metal sites. Using core-shell nanoparticles (NPs) as a building block, the Pd-FeOx NPs are transformed into a porous yolk-shell structure along with the formation of SMSIR upon treatment under a reductive atmosphere. The final structure, denoted as Pd-Fe3O4-H, exhibits excellent catalytic performance in semi-hydrogenation of acetylene with 100% conversion and 85.1% selectivity to ethylene at 80 °C. Detailed electron microscopic and spectroscopic experiments coupled with computational modeling demonstrate that the compelling performance stems from the SMSIR, favoring the formation of surface hydrogen on Pd instead of hydride.

A Method for Obtaining Liquid-Solid Adsorption Rates from Molecular Dynamics Simulations: Applied to Methanol on Pt(111) in H2O.

Adsorption is an important step in heterogeneous catalysis as it predetermines how many reactant molecules can participate in a surface reaction per unit time. While the rate of adsorption processes is well studied in gas-solid adsorption in both theory and experiment, such rates are still not well studied for liquid-solid adsorption. This is partly because the ever-changing configurations of liquid-phase solvent molecules impede the ability to study a molecule approaching a surface from a liquid phase by either experiment or theory. In this work, we develop a method using molecular dynamics (MD) simulations to study the rate of adsorption in liquid-solid adsorption processes. Specifically, we use MD to model the diffusion of a methanol molecule in aqueous solvent and its adsorption to a Pt(111) surface. We find that by approximating the solute motion as following the same displacement rates as a random walk model, the adsorbed and non-adsorbed states of the methanol molecule near the Pt(111) surface can be discerned and quantified. In particular, this methodology enables extracting a sticking coefficient and a macroscopically relatable adsorption rate. This method can be applied to arbitrary types of reactants and surfaces, as well as different liquid environments, thus providing a general tool for predicting quantitative adsorption rates of liquid-solid adsorption systems.

SQERT-T: alleviating kinetic Monte Carlo (KMC)-stiffness in transient KMC simulations.

Lattice based kinetic Monte Carlo (KMC) is often used for simulating the dynamics of systems at a supramolecular scale, based on molecular scale transitions. A common challenge in KMC simulations is rapid 'back-and-forth' reactions, which dominate the events executed during simulations and inhibit the ability for simulations to reach longer time scales. Such processes are fast frivolous processes (FFPs) and are one manifestation of a phenomenon referred to as KMC-stiffness. Here, an algorithm for staggered quasi-equilibrium rank-based throttling geared towards transient kinetics (SQERT-T) is presented. Within the SQERT-T methodology, a pace-restrictor reaction and an FFP floor are utilized along with throttling of the process transition rate constants to accelerate the KMC simulations while still retaining sufficient time resolution for sampling of the data. KMC simulations were performed for CO oxidation over RuO2(1 1 0) and over RuO2(1 1 1), and the results were compared to experimental data obtained using RuO2 powders. The experiments and simulations were for transient conditions: the system was subjected to a temperature program which included temperatures in the range of 363 to 453 K. The timescales that were achieved during the KMC simulations in this study would not have been accessible without KMC acceleration, and were enabled by the use of SQERT-T.

Below-Room-Temperature C-H Bond Breaking on an Inexpensive Metal Oxide: Methanol to Formaldehyde on CeO2(111).

Upgrading of primary alcohols by C-H bond breaking currently requires temperatures of >200 °C. In this work, new understanding from simulation of a temperature-programmed reaction study with methanol over a CeO2(111) surface shows C-H bond breaking and the subsequent desorption of formaldehyde, even below room temperature. This is of particular interest because CeO2 is a naturally abundant and inexpensive metal oxide. We combine density functional theory and kinetic Monte Carlo methods to show that the low-temperature C-H bond breaking occurs via disproportionation of adjacent methoxy species. We further show from calculations that the same transition state with comparable activation energy exists for other primary alcohols; with ethanol, 1-propanol, and 1-butanol explicitly calculated. These findings indicate a promising class of transition states to search for in seeking low-temperature C-H bond breaking over inexpensive oxides.

Catalysis beyond frontier molecular orbitals: Selectivity in partial hydrogenation of multi-unsaturated hydrocarbons on metal catalysts.

The mechanistic understanding and control over transformations of multi-unsaturated hydrocarbons on transition metal surfaces remains one of the major challenges of hydrogenation catalysis. To reveal the microscopic origins of hydrogenation chemoselectivity, we performed a comprehensive theoretical investigation on the reactivity of two α,ß-unsaturated carbonyls-isophorone and acrolein-on seven (111) metal surfaces: Pd, Pt, Rh, Ir, Cu, Ag, and Au. In doing so, we uncover a general mechanism that goes beyond the celebrated frontier molecular orbital theory, rationalizing the C═C bond activation in isophorone and acrolein as a result of significant surface-induced broadening of high-energy inner molecular orbitals. By extending our calculations to hydrogen-precovered surface and higher adsorbate surface coverage, we further confirm the validity of the "inner orbital broadening mechanism" under realistic catalytic conditions. The proposed mechanism is fully supported by our experimental reaction studies for isophorone and acrolein over Pd nanoparticles terminated with (111) facets. Although the position of the frontier molecular orbitals in these molecules, which are commonly considered to be responsible for chemical interactions, suggests preferential hydrogenation of the C═O double bond, experiments show that hydrogenation occurs at the C═C bond on Pd catalysts. The extent of broadening of inner molecular orbitals might be used as a guiding principle to predict the chemoselectivity for a wide class of catalytic reactions at metal surfaces.

Reaction efficiency effects on binary chemical reactions.

We study the effect of the variation of reaction efficiency in binary reactions. We use the well-known A + B → 0 model, which has been extensively studied in the past. We perform simulations on this model where we vary the efficiency of reaction, i.e., when two particles meet they do not instantly react, as has been assumed in previous studies, but they react with a probability γ, where γ is in the range 0 < γ < 1. Our results show that at small γ values the system is reaction limited, but as γ increases it crosses over to a diffusion limited behavior. At early times, for small γ values, the particle density falls slower than for larger γ values. This fall-off goes over a crossover point, around the value of γ = 0.50 for high initial densities. Under a variety of conditions simulated, we find that the crossover point was dependent on the initial concentration but not on the lattice size. For intermediate and long times simulations, all γ values (in the depleted reciprocal density versus time plot) converge to the same behavior. These theoretical results are useful in models of epidemic reactions and epidemic spreading, where a contagion from one neighbor to the next is not always successful but proceeds with a certain probability, an analogous effect with the reaction probability examined in the current work.

Elucidation of intermediates and mechanisms in heterogeneous catalysis using infrared spectroscopy.

Infrared spectroscopy has a long history as a tool for the identification of chemical compounds. More recently, various implementations of infrared spectroscopy have been successfully applied to studies of heterogeneous catalytic reactions with the objective of identifying intermediates and determining catalytic reaction mechanisms. We discuss selective applications of these techniques with a focus on several heterogeneous catalytic reactions, including hydrogenation, deNOx, water-gas shift, and reverse-water-gas shift. The utility of using isotopic substitutions and other techniques in tandem with infrared spectroscopy is discussed. We comment on the modes of implementation and the advantages and disadvantages of the various infrared techniques. We also note future trends and the role of computational calculations in such studies. The infrared techniques considered are transmission Fourier transform infrared spectroscopy, infrared reflection-absorption spectroscopy, polarization-modulation infrared reflection-absorption spectroscopy, sum-frequency generation, diffuse reflectance infrared Fourier transform spectroscopy, attenuated total reflectance, infrared emission spectroscopy, photoacoustic infrared spectroscopy, and surface-enhanced infrared absorption spectroscopy.

Interaction of Isophorone with Pd(111): A Combination of Infrared Reflection-Absorption Spectroscopy, Near-Edge X-ray Absorption Fine Structure, and Density Functional Theory Studies.

Atomistic level understanding of interaction of α,ß-unsaturated carbonyls with late transition metals is a key prerequisite for rational design of new catalytic materials with the desired selectivity toward C=C or C=O bond hydrogenation. The interaction of this class of compounds with transition metals was investigated on α,ß-unsaturated ketone isophorone on Pd(111) as a prototypical system. In this study, infrared reflection-absorption spectroscopy (IRAS), near-edge X-ray absorption fine structure (NEXAFS) experiments, and density functional theory calculations including van der Waals interactions (DFT+vdW) were combined to obtain detailed information on the binding of isophorone to palladium at different coverages and on the effect of preadsorbed hydrogen on the binding and adsorption geometry. According to these experimental observations and the results of theoretical calculations, isophorone adsorbs on Pd(111) in a flat-lying geometry at low coverages. With increasing coverage, both C=C and C=O bonds of isophorone tilt with respect to the surface plane. The tilting is considerably more pronounced for the C=C bond on the pristine Pd(111) surface, indicating a prominent perturbation and structural distortion of the conjugated π system upon interaction with Pd. Preadsorbed hydrogen leads to higher tilting angles of both π bonds, which points to much weaker interaction of isophorone with hydrogen-precovered Pd and suggests the conservation of the in-plane geometry of the conjugated π system. The results of the DFT+vdW calculations provide further insights into the perturbation of the molecular structure of isophorone on Pd(111).

Kinetic evidence for a non-Langmuir-Hinshelwood surface reaction: H/D exchange over Pd nanoparticles and Pd(111).

The mechanism of hydrogen recombination on a Pd(111) single crystal and well-defined Pd nanoparticles is studied using pulsed multi-molecular beam techniques and the H2/D2 isotope exchange reaction. The focus of this study is to obtain a microscopic understanding of the role of subsurface hydrogen in enhancing the associative desorption of molecular hydrogen. HD production from H2 and D2 over Pd is investigated using pulsed molecular beams, and the temperature dependence and reaction orders are obtained for the rate of HD production under various reaction conditions designed to modulate the amount of subsurface hydrogen present. The experimental data are compared to the results of kinetic modeling based on different mechanisms for hydrogen recombination. We found that under conditions where virtually no subsurface hydrogen species are present, the HD formation rate can be described exceptionally well by a classic Langmuir-Hinshelwood model. However, this model completely fails to reproduce the experimentally observed high HD formation rates and the reaction orders under reaction conditions where subsurface hydrogen is present. To analyze this phenomenon, we develop two kinetic models that account for the role of subsurface hydrogen. First, we investigate the possibility of a change in the reaction mechanism, where recombination of one subsurface and one surface hydrogen species (known as a breakthrough mechanism) becomes dominant when subsurface hydrogen is present. Second, we investigate the possibility of the modified Langmuir-Hinshelwood mechanism with subsurface hydrogen lowering the activation energy for recombination of two hydrogen species adsorbed on the surface. We show that the experimental reaction kinetics can be well described by both kinetic models based on non-Langmuir-Hinshelwood-type mechanisms.

Toward Low-Temperature Dehydrogenation Catalysis: Isophorone Adsorbed on Pd(111).

Adsorbate geometry and reaction dynamics play essential roles in catalytic processes at surfaces. Here we present a theoretical and experimental study for a model functional organic/metal interface: isophorone (C9H14O) adsorbed on the Pd(111) surface. Density functional theory calculations with the Perdew-Burke-Ernzerhoff (PBE) functional including van der Waals (vdW) interactions, in combination with infrared spectroscopy and temperature-programmed desorption (TPD) experiments, reveal the reaction pathway between the weakly chemisorbed reactant (C9H14O) and the strongly chemisorbed product (C9H10O), which occurs by the cleavage of four C-H bonds below 250 K. Analysis of the TPD spectrum is consistent with the relatively small magnitude of the activation barrier derived from PBE+vdW calculations, demonstrating the feasibility of low-temperature dehydrogenation.

A kinetic study on the conversion of cis-2-butene with deuterium on a Pd/Fe3O4 model catalyst.

The conversion of cis-2-butene with deuterium over a well-defined Pd/Fe(3)O(4) model catalyst was studied by isothermal pulsed molecular beam (MB) experiments under ultra high vacuum conditions. This study focuses on the processes related to dissociative hydrogen adsorption and diffusion into the subsurface of Pd nanoparticles and their influence on the activity and selectivity toward competing cis-trans isomerization and hydrogenation pathways. The reactivity was studied both under steady state conditions and in the transient regime, in which the reaction takes place on a D-saturated catalyst, over a large range of reactant pressures and reaction temperatures. We show that large olefin coverages negatively affect the abundance of D species, as indicated by a reduction of both reaction rates under steady state conditions as compared to the transient reactivity on the catalyst pre-saturated with D(2). Limitations in D availability during the steady state lead to a very weak dependence of both reaction rates on the olefin pressure. In contrast, when the surface is initially saturated with D, the transient reaction rates of both pathways exhibit positive kinetic orders on the butene pressure. Cis-trans isomerization and hydrogenation show kinetic orders of +0.7 and +1.0 on the D(2) pressure, respectively. Increasing availability of D noticeably shifts the selectivity toward hydrogenation. These observations together with the analysis of the transient reaction behavior suggest that the activity and selectivity of the catalyst is strongly controlled by its ability to build up and maintain a sufficiently high concentration of D species under reaction conditions. The temperature dependence of the reaction rates indicates that higher activation energies are required for the hydrogenation pathway than for the cis-trans isomerization pathway, implying that different rate limiting steps are involved in the competing reactions.

Role of hydrogen in olefin isomerization and hydrogenation: a molecular beam study on Pd model supported catalysts.

The role of surface, and subsurface hydrogen species in olefin cis-trans isomerization and hydrogenation over a model Pd/Fe(3)O(4)/Pt(111) catalyst was investigated by pulsed molecular beam experiments and infrared reflection-absorption spectroscopy. We show that non-equivalent hydrogen species are involved in the two reaction pathways: whereas cis-trans isomerization proceeds with the surface hydrogen species, the presence of hydrogen absorbed in the subsurface region of Pd particles is required for the hydrogenation pathway. The activity and selectivity toward both reaction channels was found to significantly change on Pd particles when they are modified with strongly dehydrogenated carbonaceous deposits. Sustained hydrogenation activity was observed only on C-precovered particles, whereas sustained cis-trans isomerization proceeds on both C-free and C-containing catalyst. We discuss the possible microscopic origins of this effect.

TPD of nitric acid from BaNa-Y: evidence that a nanoscale environment can alter a reaction mechanism.

The mechanism of temperature-programmed desorption (TPD) of nitric acid chemisorbed on BaNa-Y was studied over the temperature range from 200 to 400 degrees C, in the presence and absence of CO. Nitric acid dissociates to form H(+) and NO(3)(-) when chemisorbed on BaNa-Y. The results of these experiments are consistent with H(+) and NO(3)(-) either reacting directly to produce OH and NO(2) or recombining to produce HNO(3), which is desorbed and rapidly decomposes within the zeolite pores to OH and NO(2). The kinetics and stoichiometry suggest that the hydroxyl radicals produced react with CO and NO(2) to form CO(2) + H and NO + HO(2), respectively. The H atoms thus formed react with OH in preference to NO(2), a change in mechanism consistent with literature rate constants and the expectation that the zeolite pore walls act as a third body for the reaction of H with OH. Finally, OH may react with NO(2) to form HO(2), which can undergo further reactions to form O(2), H(2)O, and/or H(2). No reaction between CO and NO(3) or CO and surface-bound NO(3)(-) was observed.