Computational approaches to the determination of active site structures and reaction mechanisms in heterogeneous catalysts

The promotion effect of π-π interactions in Pd NPs catalysed selective hydrogenation

The utilization of weak interactions to improve the catalytic performance of supported metal catalysts is an important strategy for catalysts design, but still remains a big challenge. In this work, the weak interactions nearby the Pd nanoparticles (NPs) are finely tuned by using a series of imine-linked covalent organic frameworks (COFs) with different conjugation skeletons. The Pd NPs embedded in pyrene-COF are ca. 3 to 10-fold more active than those in COFs without pyrene in the hydrogenation of aromatic ketones/aldehydes, quinolines and nitrobenzene, though Pd have similar size and surface structure. With acetophenone (AP) hydrogenation as a model reaction, systematic studies imply that the π-π interaction of AP and pyrene rings in the vicinity of Pd NPs could significantly reduce the activation barrier in the rate-determining step. This work highlights the important role of non-covalent interactions beyond the active sites in modulating the catalytic performance of supported metal NPs.

The non-covalent interactions play an important role in biocatalysis, but they have not been fully explored in metal-catalysed reactions. Herein, the authors present advanced understanding of the π-π interactions of covalent organic frameworks in Pd catalysed selective hydrogenation.

Optimization of mesoporous titanosilicate catalysts for cyclohexene epoxidation via statistically guided synthesis

An efficient approach to improve the catalytic activity of titanosilicates is introduced. The Doehlert matrix (DM) statistical model was utilized to probe the synthetic parameters of mesoporous titanosilicate microspheres (MTSM), in order to increase their catalytic activity with a minimal number of experiments. Synthesis optimization was carried out by varying two parameters simultaneously: homogenizing temperature and surfactant weight. Thirteen different MTSM samples were synthesized in two sequential 'matrices' according to Doehlert conditions and were used to catalyse the epoxidation of cyclohexene with tert-butyl hydroperoxide. The samples (and the corresponding synthesis conditions) with superior catalytic activity in terms of product yield and selectivity were identified. In addition, this approach revealed the limiting values of each synthesis parameter, beyond which the material becomes catalytically ineffective. This study demonstrates that the DM approach can be broadly used as a powerful and time-efficient tool for investigating the optimal synthesis conditions of heterogeneous catalysts.

Modelling the chemistry of Mn-doped MgO for bulk and (100) surfaces

We have investigated the energetic properties of Mn-doped MgO bulk and (100) surfaces using a QM/MM embedding computational method, calculating the formation energy for doped systems, as well as for surface defects, and the subsequent effect on chemical reactivity.

Insights into Laccase Engineering from Molecular Simulations: Toward a Binding-Focused Strategy

Understanding the molecular determinants of enzyme performance is of primary importance for the rational design of ad hoc mutants. A novel approach, which combines efficient conformational sampling and quick reactivity scoring, is used here to shed light on how substrate oxidation was improved during the directed evolution experiment of a fungal laccase (from Pycnoporus cinnabarinus), an industrially relevant class of oxidoreductases. It is found that the enhanced activity of the evolved enzyme is mainly the result of substrate arrangement in the active site, with no important change in the redox potential of the T1 copper. Mutations at the active site shift the binding mode into a more buried substrate position and provide a more favorable electrostatic environment for substrate oxidation. As a consequence, engineering the binding event seems to be a viable way to in silico evolution of oxidoreductases.

The concept, reality and utility of single-site heterogeneous catalysts (SSHCs)

The large-pores of this metal–organic framework allow bulky reactants to be catalytically converted at single-site active centres situated at the inner surface.

QM/MM investigations of organic chemistry oriented questions

About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.

Gas-phase reactions of cationic vanadium-phosphorus oxide clusters with C2H(x) (x=4, 6): a DFT-based analysis of reactivity patterns

The reactivities of the adamantane-like heteronuclear vanadium-phosphorus oxygen cluster ions [V(x)P(4-x)O(10)](.+) (x=0, 2-4) towards hydrocarbons strongly depend on the V/P ratio of the clusters. Possible mechanisms for the gas-phase reactions of these heteronuclear cations with ethene and ethane have been elucidated by means of DFT-based calculations; homolytic C-H bond activation constitutes the initial step, and for all systems the P-O(.) unit of the clusters serves as the reactive site. More complex oxidation processes, such as oxygen-atom transfer to, or oxidative dehydrogenation of the hydrocarbons require the presence of a vanadium atom to provide the electronic prerequisites which are necessary to bring about the 2e(-) reduction of the cationic clusters.

Curvature correction for microiterative optimizations with QM/MM electronic embedding

One of the most common methods to treat the electrostatic effect of the environment in QM/MM calculations is to include the MM atoms as point charges in the QM Hamiltonian. In this case, a microiterative geometry optimization ignoring the QM contributions to the forces in the relaxation of the environment cannot yield exact stationary points. One solution that has been suggested in the literature is based on using a constant additive correction to the MM gradient during the microiterations, determined in the preceding macroiteration. Here, we analyze the convergence properties of the gradient correction method and point out that a smooth relaxation is not ensured if the curvature of the approximate, MM-based description of the potential energy surface of the environment is too small in comparison with the exact one. We suggest a computationally cheap second-order correction that uses an estimated Hessian from the Davidon-Fletcher-Powell method to tackle the problems caused by the too small curvature. Test calculations on four metalloenzymatic systems (∼100 QM atoms, ∼2000 relaxed MM atoms, ∼20,000 atoms in total) show that our approach efficiently restores the convergence where gradient correction alone would lead to oscillations.

The societal significance of catalysis and the growing practical importance of single-site heterogeneous catalysts

The concept of single-site heterogeneous catalysis, herein defined and extensively illustrated, offers a strategy for the design of new solid catalysts. By capitalizing on the opportunities presented by nanoporous materials to assemble a wide range of new, well-defined, catalytically active centres, it is possible to bring about numerous environmentally benign processes that can replace traditional methods of chemical production. The latter often employs aggressive, corrosive or hazardous reagents. By using both microporous (less than 20 Å diameter) and mesoporous solids (20–500 Å diameter), abundant scope exists for the construction and application of shape-selective, regio-selective and enantioselective catalysts.

Aerobic oxidation of hydrocarbons in Mn-doped aluminophosphates: a computational perspective to understand mechanism and selectivity

We discuss the mechanism and energetics for the aerobic oxidation of hydrocarbons catalysed by Mn-doped nanoporous aluminophosphates with the AFI structure (Mn-APO-5), obtained computationally using electronic structure techniques. Calculations have been performed employing hybrid exchange density functional theory methods under periodic boundary conditions. The active sites of the catalyst are tetrahedral Mn ions isomorphously replacing Al in the microporous crystalline framework of the AlPO host. Since all Al sites in AFI are symmetry equivalent, all Mn dopants are in an identical chemical and structural environment, and hence satisfy the definition of a single-site heterogeneous catalyst. We focus in particular on the atomic-level origin of selectivity in this catalytic reaction.

Chemistry with methane: concepts rather than recipes

Four seemingly simple transformations related to the chemistry of methane will be addressed from mechanistic and conceptual points of view: 1) metal-mediated dehydrogenation to form metal carbene complexes, 2) the hydrogen-atom abstraction step in the oxidative dimerization of methane, 3) the mechanisms of the CH(4)→CH(3)OH conversion, and 4) the initial bond scission (C-H vs. O-H) as well as the rate-limiting step in the selective CH(3)OH→CH(2)O oxidation. State-of-the-art gas-phase experiments, in conjunction with electronic-structure calculations, permit identification of the elementary reactions at a molecular level and thus allow us to unravel detailed mechanistic aspects. Where appropriate, these results are compared with findings from related studies in solution or on surfaces.

Characterization of hydrogen dissociation over aluminium-doped zinc oxide using an efficient massively parallel framework for QM/MM calculations

A task-farm parallelization framework has been implemented in the ChemShell computational chemistry environment to provide a facility for parallelizing common chemical calculations, including finite-difference Hessian evaluation, the nudged elastic band method for reaction path optimization, and population-based methods for global optimization. The optimization methods are provided by a parallel interface to the DL-FIND optimization library. As ChemShell can already exploit parallel external programs for energy and gradient evaluations, the new methods result in a two-level approach to parallelization that gives significantly improved performance for massively parallel calculations. For typical systems, speed-up factors of five to eight times have been observed compared with non-task-farmed calculations. The task-farming version of ChemShell has been used to study the heterolytic dissociation of a hydrogen molecule over a polar oxygen-terminated surface of aluminium-doped zinc oxide using an embedded cluster hybrid QM/MM approach. We calculate a 42 kcal mol −1 heat of reaction and a 30 kcal mol −1 activation energy, which is equivalent to a high backward reaction barrier of 72 kcal mol −1 per H 2 molecule, in close agreement with temperature programmed desorption experiments. The dissociation path includes a stable intermediate comprising a hydride ion in an oxygen vacancy and physisorbed atomic hydrogen.

Advances in computational studies of energy materials

We review recent developments and applications of computational modelling techniques in the field of materials for energy technologies including hydrogen production and storage, energy storage and conversion, and light absorption and emission. In addition, we present new work on an Sn2TiO4 photocatalyst containing an Sn(II) lone pair, new interatomic potential models for SrTiO3 and GaN, an exploration of defects in the kesterite/stannite-structured solar cell absorber Cu2ZnSnS4, and report details of the incorporation of hydrogen into Ag2O and Cu2O. Special attention is paid to the modelling of nanostructured systems, including ceria (CeO2, mixed Ce(x)O(y) and Ce2O3) and group 13 sesquioxides. We consider applications based on both interatomic potential and electronic structure methodologies; and we illustrate the increasingly quantitative and predictive nature of modelling in this field.

Density functional theory for transition metals and transition metal chemistry

We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids.

QM/MM methods for biomolecular systems

Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.

Heterogeneous catalysis: enigmas, illusions, challenges, realities, and emergent strategies of design

Predominantly this article deals with the question of how to design new solid catalysts for a variety of industrial and laboratory-orientated purposes. A generally applicable strategy, illustrated by numerous examples, is made possible based on the use of nanoporous materials on to the (high-area) inner surfaces of which well-defined (experimentally and computationally) active centers are placed in a spatially separated fashion. Such single-site catalysts, which have much in common with metal-centered homogenous catalysts and enzymes, enable a wide range of new catalysts to be designed for a variety of selective oxidations, hydrogenations, hydrations and hydrodewaxing, and other reactions that the "greening" of industrial processes demand. Examples are given of new shape-selective, regio-selective, and enantioselective catalysts, many of which operate under mild, environmentally benign conditions. Also considered are some of the reasons why detailed studies of adsorption and stoichiometric reactions at single-crystal surfaces have, disappointingly, not hitherto paved the way to the design and production of many new heterogeneous catalysts. Recent work of a theoretical and high-throughout nature, allied to some experimental studies of well-chosen model systems, holds promise for the identification of new catalysts for simple, but industrially important reactions.