S. T. Bromley

QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis

Abstract We describe the work of the European project QUASI (Quantum Simulation in Industry, project EP25047) which has sought to develop a flexible QM/MM scheme and to apply it to a range of industrial problems. A number of QM/MM approaches were implemented within the computational chemistry scripting system, ChemShell, which provides the framework for deploying a variety of independent program packages. This software was applied in several large-scale QM/MM studies which addressed the catalytic decomposition of N 2 O by Cu-containing zeolites, the methanol synthesis reaction catalysed by Cu clusters supported on ZnO surfaces, and the modelling of enzyme structure and reactivity.

New insights into the structure of supported bimetallic nanocluster catalysts prepared from carbonylated precursors: a combined density functional theory and EXAFS study

Abstract An ensemble of Ru 12 Cu 4 C 2 bimetallic clusters derived from organometallic precursors and anchored within mesoporous silica is investigated with molecular mechanics (MM) and ab initio techniques. The computational study, guided by experiment, yields a representative cluster structure which is compared with EXAFS data. The comparison yields possible insights into the effects of cluster structure upon the thermal decomposition of the carbonyl ligands. Density functional theory (DFT) calculations suggest an unexpected structural modification of the silica-supported cluster upon removal of the attendent carbonyl ligands, in particular the displacement of the central carbido atoms.

Molecular-dynamics analysis of the diffusion of molecular hydrogen in all-silica sodalite

In order to investigate the technical feasibility of crystalline porous silicates as hydrogen storage materials, the self-diffusion of molecular hydrogen in all-silica sodalite is modeled using large-scale classical molecular-dynamics simulations employing full lattice flexibility. In the temperature range of 700-1200 K, the diffusion coefficient is found to range from 1.610(-10) to 1.810(-9) m(2)/s. The energy barrier for hydrogen diffusion is determined from the simulations allowing the application of transition state theory, which, together with the finding that the pre-exponential factor in the Arrhenius-type equation for the hopping rate is temperature-independent, enables extrapolation of our results to lower temperatures. Estimates based on mass penetration theory calculations indicate a promising hydrogen uptake rate at 573 K.

Assignment of the complex vibrational spectra of the hydrogenated ZnO polar surfaces using QM/MM embedding

Hydrogenated zinc oxide gives rise to complex vibrational spectra with many prominent features that remain unexplained. Our calculations have unambiguously shown that the presence of vacant oxygen and zinc interstitial surface sites is the only way to rationalize the observed spectra, notably the 1710 cm−1 zinc hydride stretching mode. The large number of such sites, which expose low-coordinated surface ions, are inherent at ionically reconstructed polar surfaces. The thermal stability of the sorbed hydrogen and the infrared activity of the resulting species are correlated with site coordination and coverage.

Molecular modelling of the transport behaviour of C3 and C4 gases through the zeolite DD3R

Abstract The all-silica zeolite deca-dodecasil 3R (DD3R) has a two-dimensional pore structure which might be used for separation of gas mixtures of small molecules in a zeolite packed bed or membrane configuration. The DD3R pore structure exists of large cages connected by narrow 8-membered oxygen rings. A specially developed and computationally efficient molecular modelling method is used to determine the permeability of a number of gaseous C 3 and C 4 hydrocarbon compounds in a DD3R zeolite membrane. The permeability is determined by the solubility coefficient and the diffusion coefficient. The solubility coefficient is determined from the adsorption energy of a gas molecule in the DD3R cage. The diffusion coefficient is determined from the energy barrier for diffusion which is the energy difference of the gas molecule in the ring and in the cage. High permeabilities and selectivities for the compounds trans -1,3-butadiene and propene were determined.

Preparation and characterisation of a highly active bimetallic (Pd–Ru) nanoparticle heterogeneous catalyst†

The mixed-metal carbonylate cluster [Pd6Ru6(CO)24]2– was used as a single-source precursor in the synthesis of a highly active hydrogenation catalyst (stoichiometry PdRu) which has been characterised by electron microscopy and X-ray absorption spectroscopy: PdRu readily hydrogenates alkenes and naphthalene (the latter predominantly to cis- decalin) under mild conditions

Effect of cation distribution on self-diffusion of molecular hydrogen in Na3Al3Si3O12 sodalite: a molecular dynamics study.

The diffusion of hydrogen in sodium aluminum sodalite (NaAlSi-SOD) is modeled using classical molecular dynamics, allowing for full flexibility of the host framework, in the temperature range 800-1200 K. From these simulations, the self-diffusion coefficient is determined as a function of temperature and the hydrogen uptake at low equilibrium hydrogen concentration is estimated at 573 K. The influence of the cation distribution over the framework on the hydrogen self-diffusion is investigated by comparing results employing a low energy fully ordered cation distribution with those obtained using a less ordered distribution. The cation distribution is found to have a surprisingly large influence on the diffusion, which appears to be due to the difference in framework flexibility for different cation distributions, the occurrence of correlated hopping in case of the ordered distribution, and the different nature of the diffusion processes in both systems. Compared to our previously reported calculations on all silica sodalite (all-Si-SOD), the hydrogen diffusion coefficient of sodium aluminum sodalite is higher in the case of the ordered distribution and lower in case of the disordered distribution. The hydrogen uptake rates of all-Si-SOD and NaSiAl-SOD are comparable at high temperatures (approximately 1000 K) and lower for all-Si-SOD at lower temperatures (approximately 400 K).

Two-ring vibrational modes on silica surfaces investigated via fully coordinated nanoclusters

Abstract Vibrational modes of rings containing two silicon atoms and two oxygen atoms, two-rings, as found on a variety of silica surfaces, are modelled with fully connected (SiO2)12 clusters containing no terminating groups. Such clusters naturally reflect the embedding of surface two-rings in a silica matrix without the need for large calculations of silica surface layers. The relatively small size of the clusters allows us to employ the recommended high levels of theory for vibrational calculations, but are sufficiently large to study a range of two-ring-containing conformations. The calculated spectra for the clusters display many peaks in the experimental window, with some in excellent frequency and intensity agreement with measured bands. The results are discussed with respect to the structural nature of the clusters and the possibility of collective two-ring surface modes.

Bimetallic clusters supported on mesoporous silica: the effects of support interactions on cluster morphology

Small bimetallic clusters supported on mesoporous silica have proved to be exceptionally active as hydrogenation catalysts [Amer. Philos. Soc. 388 (1999) 143]. Such catalysts are often extremely stable, especially when containing either copper or silver as one of their chemical constituents, forming arrays of strongly anchored discrete clusters [Angew. Chem. Int. Ed. Engl. 36 (1997) 2242, Chem. fur. J. 4 (1998) 1214]. Here, we show, using density functional theory (DFT), how different modes of anchoring can influence the morphology of the supported cluster. Together with extended X-ray absorbtion fine spectra (EXAFS) analysis, these DFT simulations have yielded the most favourable cluster-silica bonding scenario for the Ru12Cu4C2 nanoparticle catalyst

Computational modeling of active sites in heterogeneous catalysts

Industrial catalysts often owe their remarkable activity, selectivity and reliability to many years of gradual improvement and optimization. Such research largely relies on physically/chemically motivated systematic variations of important parameters such as catalyst composition and working conditions, but often there is only moderate emphasis placed on the elucidation of the fundamental reasons for a catalysts success. This “trial-and-error” approach is chosen not because of any strong reluctance to discover a catalysts intrinsic workings but, rather, because modern catalysts are extremely complicated systems, making fundamental investigations expensive in time and money and with no guarantee of useful results. One reason for this is that, from the theoretical analysis point of view regarding such complex systems, it can appear almost impossible to distinguish the catalytically important and active aspects from the redundant and passive. The assumption that this division of role can be made, however, lies at the root of most intuitive ideas relating to catalytic activity. In this article, we aim to illustrate that by combining computational approaches with this conceptual division of role much benefit can be derived. Such considerations are based around the general concept of localized active sites, as distinguished from the supporting liquid or solid environments of the catalyst, which are assumed to be relatively inert but not without influence. We will show how this concept can be used as the starting point of modern computational modeling techniques, which can be applied at a number of different levels to heterogeneous catalytic systems, pointing the way to a more efficient approach to catalyst optimization and understanding than trial-and-error. Our account will culminate in one of the most computationally extensive descriptions of an active site yet achieved.