Adaptive kinetic Monte Carlo simulations of surface segregation in PdAu nanoparticles.

Surface segregation in bimetallic nanoparticles (NPs) is critically important for their catalytic activity because the activity is largely determined by the surface composition. Little, however, is known about the atomic scale mechanisms and kinetics of surface segregation. One reason is that it is hard to resolve atomic rearrangements experimentally. It is also difficult to model surface segregation at the atomic scale because the atomic rearrangements can take place on time scales of seconds or minutes - much longer than can be modeled with molecular dynamics. Here we use the adaptive kinetic Monte Carlo (AKMC) method to model the segregation dynamics in PdAu NPs over experimentally relevant time scales, and reveal the origin of kinetic stability of the core@shell and random alloy NPs at the atomic level. Our focus on PdAu NPs is motivated by experimental work showing that both core@shell and random alloy PdAu NPs with diameters of less than 2 nm are stable, indicating that one of these structures must be metastable and kinetically trapped. Our simulations show that both the Au@Pd and the PdAu random alloy NPs are metastable and kinetically trapped below 400 K over time scales of hours. These AKMC simulations provide insight into the energy landscape of the two NP structures, and the diffusion mechanisms that lead to segregation. In the core-shell NP, surface segregation occurs primarily on the (100) facet through both a vacancy-mediated and a concerted mechanism. The system becomes kinetically trapped when all corner sites in the core of the NP are occupied by Pd atoms. Higher energy barriers are required for further segregation, so that the metastable NP has a partially alloyed shell. In contrast, surface segregation in the random alloy PdAu NP is suppressed because the random alloy NP has reduced strain as compared to the Au@Pd NP, and the segregation mechanisms in the alloy require more elastic energy for exchange of Pd and Au and between the surface and subsurface.

Lithium promoted mesoporous manganese oxide catalyzed oxidation of allyl ethers.

Herein we report the first example of the catalytic aerobic partial oxidation of allyl ether to its acrylate ester derivative. Many partial oxidations often need an expensive oxidant such as peroxides or other species to drive such reactions. In addition, selective generation of esters using porous catalysts has been elusive. This reaction is catalyzed by a Li ion promoted mesoporous manganese oxide (meso-Mn2O3) under mild conditions with no precious metals, a reusable heterogeneous catalyst, and easy isolation. This process is very attractive for the oxidation of allyl ethers. We report on the catalytic activity, selectivity, and scope of the reaction. In the best cases presented, almost complete conversion of allyl ether with near complete chemo-selectivity towards acrylate ester derivatives is observed. Based on results from controlled experiments, we propose a possible reaction mechanism for the case in which N-hydroxyphthalimide (NHPI) is used in combination with trichloroacetonitrile (CCl3CN).

Heterogeneous Catalytic Oxidation of Amides to Imides by Manganese Oxides.

Herein, we report a one-step peroxide mediated heterogeneous catalytic oxidation of amides to imides utilizing a series of manganese oxides. Among them, Cs/Mn2O3 was found to be the most active catalyst for the selective partial oxidation of N-benzylbenzamide to diphenyl imide. We have been able to apply an optimized oxidation method to other aromatic substrates. The feasibility of using air as an oxidant, the heterogeneous nature, inexpensive catalytic materials, respectable turnover numbers, and chemoselectivity to imides make this methodology an attractive choice for functional group transformations of amides to imides.

Development of a ReaxFF Reactive Force Field for the Pt-Ni Alloy Catalyst.

We developed the ReaxFF force field for Pt/Ni/C/H/O interactions, specifically targeted for heterogeneous catalysis application of the Pt-Ni alloy. The force field is trained using the DFT data for equations of state of Pt3Ni, PtNi3 and PtNi alloys, the surface energy of the PtxNi1-x(111) (x = 0.67-0.83), and binding energies of various atomic and molecular species (O, H, C, CH, CH2, CH3, CO, OH, and H2O) on these surfaces. The ReaxFF force field shows a Pt surface segregation at x ≥ 0.67 for the (111) surface and x ≥ 0.62 for the (100) surface in vacuum. In addition, from the investigation of the preferential alloy component of the adsorbates, it is expected that H and CH3 on the alloy surface to induce a segregation of Pt whereas the oxidation intermediates and products such as C, O, OH, H2O, CO, CH, and CH2 are found to induce Ni segregation. The relative order of binding strengths among adsorbates is a function of alloy composition and the force field is trained to describe the trend observed in DFT calculations, namely, H2 < H2O < CH3 ≈ O2 ≈ CO < OH < CH2 < C ≈ CH on Pt8Ni4, H2 < H2O < CO ≈ O2 < CH3 < OH < CH2 < CH < C on Pt9Ni3, and H2 < H2O < O2 < CO < CH3 < OH < CH2 < C ≈ CH on Pt10Ni2. Using this force field, we performed the grand-canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulations for a Pt3Ni slab and a truncated cuboctahedral nanoparticle terminated by (111) and (100) faces, to examine the surface segregation trend under different gas environments. It is found that Pt segregates to the alloy surface when the surface is exposed to vacuum and/or H2 environment while Ni segregates under the O2 environment. These results suggest that the Pt/Ni alloy force field can be successfully used for the preparation of Pt-Ni nanobimetallic catalysts structure using GCMC and run MD simulations to investigate its role and the catalytic chemistry in catalytic oxidation, dehydrogenation and coupling reactions. The current Pt/Ni force field still is found to have difficulties in describing the observed segregation trend in Ni-rich alloy compositions (x < 0.6), suggesting the need for additional force field training and evaluation for its application to describe the characteristics and chemistry of Ni-rich alloys.

Interactions of hydrogen with the iron and iron carbide interfaces: a ReaxFF molecular dynamics study.

Hydrogen embrittlement (HE) is a well-known material phenomenon that causes significant loss in the mechanical strength of structural iron and often leads to catastrophic failures. In order to provide a detailed atomistic description of HE we have used a reactive bond order potential to adequately describe the diffusion of hydrogen as well as its chemical interaction with other hydrogen atoms, defects, and the host metal. The currently published ReaxFF force field for Fe/C/H systems was originally developed to describe Fischer-Tropsch (FT) catalysis [C. Zou, A. C. T. van Duin and D. C. Sorescu, Top. Catal., 2012, 55, 391-401], and especially had been trained for surface formation energies, binding energies of small hydrocarbon radicals on different surfaces of iron and the barrier heights of surface reactions. We merged this force field with the latest ReaxFF carbon parameters [S. Goverapet Srinivasan, A. C. T. van Duin and P. Ganesh, J. Phys. Chem. A, 2015, 119, 1089-5639] and used the same training data set to refit the Fe/C interaction parameters. The present work is focused on evaluating the applicability of this reactive force field to describe material characteristics and study the role of defects and impurities in the bulk and at the precipitator interfaces. We study the interactions of hydrogen with pure and defective α-iron (ferrite), Fe3C (cementite), and ferrite-cementite interfaces with a vacancy cluster. We also investigate the growth of nanovoids in α-iron using a grand canonical Monte Carlo (GCMC) scheme. The calculated hydrogen diffusion coefficients for both ferrite and cementite phases predict a decrease in the work of separation with increasing hydrogen concentration at the ferrite-cementite interface, suggesting a hydrogen-induced decohesion behavior. Hydrogen accumulation at the interface was observed during molecular dynamics (MD) simulations, which is consistent with experimental findings. These results demonstrate the ability of the ReaxFF potential to elucidate various aspects of hydrogen embrittlement in α-iron and hydrogen interactions at a more complex metal/metal carbide interface.

Accurate electronic and chemical properties of 3d transition metal oxides using a calculated linear response U and a DFT + U(V) method.

We validate the usage of the calculated, linear response Hubbard U for evaluating accurate electronic and chemical properties of bulk 3d transition metal oxides. We find calculated values of U lead to improved band gaps. For the evaluation of accurate reaction energies, we first identify and eliminate contributions to the reaction energies of bulk systems due only to changes in U and construct a thermodynamic cycle that references the total energies of unique U systems to a common point using a DFT + U(V) method, which we recast from a recently introduced DFT + U(R) method for molecular systems. We then introduce a semi-empirical method based on weighted DFT/DFT + U cohesive energies to calculate bulk oxidation energies of transition metal oxides using density functional theory and linear response calculated U values. We validate this method by calculating 14 reactions energies involving V, Cr, Mn, Fe, and Co oxides. We find up to an 85% reduction of the mean average error (MAE) compared to energies calculated with the Perdew-Burke-Ernzerhof functional. When our method is compared with DFT + U with empirically derived U values and the HSE06 hybrid functional, we find up to 65% and 39% reductions in the MAE, respectively.

Reactive molecular simulations of protonation of water clusters and depletion of acidity in H-ZSM-5 zeolite.

Using reactive molecular dynamics (RMD), we present an atomistic insight into the interaction between water molecules and acidic centers of H-ZSM-5 zeolite. The reactive force field method, ReaxFF, was used to evaluate the adsorption and diffusion of water as well as to study the protonation of water molecules inside zeolite channels. The existing Si/Al/O/H parameters were refitted against DFT calculations to improve the ReaxFF description of interaction between water molecules and the acidic sites of zeolites. The diffusion coefficient of water in the zeolite obtained from refitted parameters is in excellent agreement with experimental results. The molecular dynamics (MD) simulations indicate that protonation of water molecules and acidity of the zeolite catalyst depend on water loadings and temperature and the observed trends compare favorably with existing experimental and theoretical studies. At higher water loadings, protonation of water molecules is more frequent leading to formation and growth of protonated water clusters inside zeolite channels. From the analysis of various reaction channels that were observed during the simulations, we found that such water clusters have relatively short life due to frequent interchange of protons and water molecules among the water clusters. Such proton hopping events play a key role in moving the protons between different acidic centers of zeolite. These simulations show the capability of ReaxFF in providing atomistic details of complex chemical interactions between the water phase and solid acid zeolites.

Large-scale reactive molecular dynamics simulation and kinetic modeling of high-temperature pyrolysis of the Gloeocapsomorphaprisca microfossils.

The ability to predict accurately the thermal conversion of complex carbonaceous materials is of value in both petroleum exploration and refining operations. Modeling the thermal cracking of kerogen under basinal heating conditions improves the predrill prediction of oil and gas yields and quality, thereby ultimately lowering the exploration risk. Modeling the chemical structure and reactivity of asphaltene from petroleum vacuum residues enables prediction of coke formation and properties in refinery processes, thereby lowering operating cost. The chemical structure-chemical yield modeling (CS-CYM) developed by Freund et al. is more rigorous, time-consuming, and requires a great deal of chemical insight into reaction network and reaction kinetics. The present work explores the applicability of a more fundamental atomistic simulation using the quantum mechanically based reactive force field to predict the product yield and overall kinetics of decomposition of two biopolymers, namely, the Kukersite and Gutternberg. Reactive molecular dynamics (RMD) simulations were performed on systems consisting of 10(4) to 10(5) atoms at different densities and temperatures to derive the overall kinetic parameters and a lumped kinetic model for pyrolysis. The kinetic parameters derived from the simulated pyrolysis of an individual component and the mixture of all four components in Guttenberg reveal the role of cross-talk between the fragments and enhanced reactivity of component A by radicals from other components. The Arrhenius extrapolation of the model yields reasonable prediction for the overall barrier for cracking. Because simulations were run at very high temperature (T > 1500 K) to study cracking within the simulation time of up to 1 ns, it, however, led to the entropically favored ethylene formation as a dominant decomposition route. Future work will focus on evaluating the applicability of accelerated reactive MD approaches to study cracking.

Intramolecular hydrogen migration in alkylperoxy and hydroperoxyalkylperoxy radicals: accurate treatment of hindered rotors.

We have calculated the thermochemistry and rate coefficients for stable molecules and reactions in the title reaction families using CBS-QB3 and B3LYP/CBSB7 methods. The accurate treatment of hindered rotors for molecules having multiple internal rotors with potentials that are not independent of each other can be problematic, and a simplified scheme is suggested to treat them. This is particularly important for hydroperoxyalkylperoxy radicals (HOOQOO). Two new thermochemical group values are suggested in this paper, and with these values, the group additivity method for calculation of enthalpy as implemented in reaction mechanism generator (RMG) gives good agreement with CBS-QB3 predictions. The barrier heights follow the Evans-Polanyi relationship for each type of intramolecular hydrogen migration reaction studied.

Predicted reaction rates of H(x)N(y)O(z) intermediates in the oxidation of hydroxylamine by aqueous nitric acid.

This work reports computed rate coefficients of 90 reactions important in the autocatalytic oxidation of hydroxylamine in aqueous nitric acid. Rate coefficients were calculated using four approaches: Smoluchowski (Stokes-Einstein) diffusion, a solution-phase incarnation of transition state theory based on quantum chemistry calculations, simple Marcus theory for electron-transfer reactions, and a variational TST approach for dissociative isomerization reactions that occur in the solvent cage. Available experimental data were used to test the accuracy of the computations. There were significant discrepancies between the computed and experimental values for some key parameters, indicating a need for improvements in computational methodology. Nonetheless, the 90-reaction mechanism showed the ability to reproduce many of the trends seen in experimental studies of this very complicated kinetic system. This work highlights reactions that may govern the system evolution and branching behavior critical to the stability of the system. We hope that this analysis will guide experimental investigations to reduce the uncertainties in the critical rate coefficients and thermochemistry, allowing an unambiguous determination of the dominant reaction pathways in the system. Advances in efficient and accurate solvation models that effectively separate entropic and enthalpic contributions will most directly benefit solution-phase modeling efforts. Methods for more accurately estimating activity coefficients, including at infinite dilution in multicomponent mixtures, are needed for modeling high ionic strength aqueous systems. A detailed derivation of the solution-phase equilibrium and transition state theory rate expressions in solution is included in the Supporting Information.

Thermodynamic calculations for molecules with asymmetric internal rotors. II. Application to the 1,2-dihaloethanes.

The thermodynamic properties of three halocarbon molecules relevant in atmospheric and public health applications are presented from ab initio calculations. Our technique makes use of a reaction path-like Hamiltonian to couple all the vibrational modes to a large-amplitude torsion for 1,2-difluoroethane, 1,2-dichloroethane, and 1,2-dibromoethane, each of which possesses a heavy asymmetric rotor. Optimized ab initio energies and Hessians were calculated at the CCSD(T) and MP2 levels of theory, respectively. In addition, to investigate the contribution of electronically excited states to thermodynamic properties, several excited singlet and triplet states for each of the halocarbons were computed at the CASSCF/MRCI level. Using the resulting potentials and projected frequencies, the couplings of all the vibrational modes to the large-amplitude torsion are calculated using the new STAR-P 2.4.0 software platform that automatically parallelizes our codes with distributed memory via a familiar MATLAB interface. Utilizing the efficient parallelization scheme of STAR-P, we obtain thermodynamic properties for each of the halocarbons, with temperatures ranging from 298.15 to 1000 K. We propose that the free energies, entropies, and heat capacities obtained from our methods be used to supplement theoretical and experimental values found in current thermodynamic tables.

Ab initio aqueous thermochemistry: application to the oxidation of hydroxylamine in nitric acid solution.

Ab initio molecular orbital calculations were performed and thermochemical parameters estimated for 46 species involved in the oxidation of hydroxylamine in aqueous nitric acid solution. Solution-phase properties were estimated using the several levels of theory in Gaussian03 and using COSMOtherm. The use of computational chemistry calculations for the estimation of physical properties and constants in solution is addressed. The connection between the pseudochemical potential of Ben-Naim and the traditional standard state-based thermochemistry is shown, and the connection of these ideas to computational chemistry results is established. This theoretical framework provides a basis for the practical use of the solution-phase computational chemistry estimates for real systems, without the implicit assumptions that often hide the nuances of solution-phase thermochemistry. The effect of nonidealities and a method to account for them is also discussed. A method is presented for estimating the solvation enthalpy and entropy for dilute aqueous solutions based on the solvation free energy from the ab initio calculations. The accuracy of the estimated thermochemical parameters was determined through comparison with (i) enthalpies of formation in the gas phase and in solution, (ii) Henry's law data for aqueous solutions, and (iii) various reaction equilibria in aqueous solution. Typical mean absolute deviations (MAD) for the solvation free energy in room-temperature water appear to be ~1.5 kcal/mol for most methods investigated. The MAD for computed enthalpies of formation in solution was 1.5-3 kcal/mol, depending on the methodology employed and the type of species (ion, radical, closed-shell) being computed. This work provides a relatively simple and unambiguous approach that can be used to estimate the thermochemical parameters needed to build detailed ab initio kinetic models of systems in aqueous solution. Technical challenges that limit the accuracy of the estimates are highlighted.

Thermodynamic calculations for molecules with asymmetric internal rotors--application to 1,3-butadiene.

We present quantum mechanical partition functions, free energies, entropies, and heat capacities of 1,3-butadiene derived from ab initio calculations. Our technique makes use of a reaction path-like Hamiltonian to couple all 23 vibrational modes to the large-amplitude torsion, which involves heavy asymmetric functional groups. Ab initio calculations were performed at the B3LYP, MP2, and CCSD(T) levels of theory and compared with experimental values as a reference case. By using the ab initio potentials and projected frequencies, simple perturbative expressions are presented for computing the couplings of all the vibrational modes to the large-amplitude torsion. The expressions are particularly suited for programming in the new STAR-P software platform which automatically parallelizes our codes with distributed memory via a familiar MATLAB interface. Using the efficient parallelization scheme of STAR-P, we obtain thermodynamic properties of 1,3-butadiene for temperatures ranging from 50 to 500 K. The free energies, entropies, and heat capacities obtained from our perturbative formulas are compared with conventional approximations and experimental values found in thermodynamic tables.

Oxidation of hydroxylamine by nitrous and nitric acids. Model development from first principle SCRF calculations.

Ab initio molecular orbital calculations have been performed to develop an elementary reaction mechanism for the autocatalytic and scavenging reactions of hydroxylamine in an aqueous nitric acid medium. An improved understanding of the titled reactions is needed to determine the "stability boundary of hydroxylamine" for safe operations of the plutonium-uranium reduction extraction (PUREX) process. Under the operating conditions of the PUREX process, namely, 6 M nitric acid, the reactive forms of hydroxylamine are NH2OH, NH3OH+, and the complex NH3OH.NO3, and those of nitrous acid are NO+, H2ONO+, N2O4, N2O3, NO2, and NO. High-level CBSQB3/IEFPCM and CBSQB3/COSMO calculations were performed using GAUSSIAN03 to investigate the energy landscape and to explore a large number of possible ion-ion, ion-radical, ion-molecule, radical-radical, radical-molecule, and molecule-molecule pathways available to the reactive forms of the reactants in solution. It was found that in solution the autocatalytic generation of nitrous acid proceeds through free radical pathways at low-hydroxylamine concentrations from unprotonated NH2OH via hydrogen abstraction. At high [NH3OH+], we suggest a possible involvement of the NH3ONO+ intermediate via the reaction NH2ONO + NO2 --> HNO + HONO + NO. The NH3ONO+ intermediate, in turn, is formed favorably via the ion-ion reactions of NH3OH+ with NO+ and/or the reaction between NO+ and hydroxylammonium nitrate (HAN). The intermediates involved in the scavenging reaction of nitrous acid by hydroxylamine are NH3ONO+, NH2ONO, NH2(NO)O, NH(NO)OH, and HONNOH and the rate-determining step is the 1,2-NO migration in NH2ONO leading to NH2(NO)O. Reactions NH2ONO --> NH2(NO)O and NH2(NO)O --> NH(NO)OH were studied with two explicit water molecules and the results are discussed in the context of the importance of the explicit treatment of solvent in the determination of the energetics and mechanism of these processes. The rate constants for the reactions were estimated using transition-state theory and other traditional techniques. The kinetic parameters obtained at the B3LYP/CBSB7/IEFPCM level are in reasonable agreement with the limited experimental value. IEFPCM results on free energy of undelocalized polar ions such as NO3-, NO2-, and NH3OH+ are not very accurate and have difficulties in predicting the right direction of acid dissociation equilibrium of HONO2, HONO, and NH3OH+. Explicit incorporation of a solvation shell to these ions improves the theoretical descriptions of acid ionization equilibria as it captures some of the nonlocal effects of these ions. Additional work is needed to correctly describe the solvation shell and to introduce consistency in the theoretical treatment involving explicit solvent molecules. Nevertheless, this systematic exploration of reactions in solution and mechanism development for a solution phase process based on self-consistent reaction field (SCRF) results is likely to be one of the first of its kind.