QM/MM Study on the Catalytic Mechanism of Benzene Hydroxylation over Fe−ZSM-5

The application of QM/MM simulations in heterogeneous catalysis

The QM/MM simulation method is provenly efficient for the simulation of biological systems, where an interplay of extensive environment and delicate local interactions drives a process of interest through a funnel on a complex energy landscape. Recent advances in quantum chemistry and force-field methods present opportunities for the adoption of QM/MM to simulate heterogeneous catalytic processes, and their related systems, where similar intricacies exist on the energy landscape. Herein, the fundamental theoretical considerations for performing QM/MM simulations, and the practical considerations for setting up QM/MM simulations of catalytic systems, are introduced; then, areas of heterogeneous catalysis are explored where QM/MM methods have been most fruitfully applied. The discussion includes simulations performed for adsorption processes in solvent at metallic interfaces, reaction mechanisms within zeolitic systems, nanoparticles, and defect chemistry within ionic solids. We conclude with a perspective on the current state of the field and areas where future opportunities for development and application exist.

DFT Study on the Catalytic Activity of ALD-Grown Diiron Oxide Nanoclusters for Partial Oxidation of Methane to Methanol

Using density functional theory (DFT), we studied the catalytic activity of iron oxide nanoclusters that mimic the structure of the active site in the soluble form of methane monooxygenase (sMMO) for the partial oxidation of methane to methanol. Using N₂O as the oxidant, we consider a radical-rebound mechanism and a concerted mechanism for the oxidation of methane on either a bridging oxygen (O_b) or a terminal oxygen (O_t) active site. We find that the radical-rebound pathway is preferred over the concerted pathway by 40-50 kJ/mol, but the desorption of methanol and the regeneration of the oxygen site are found to be the highest barriers for the direct conversion of methane to methanol with these catalysts. As demonstrated by a population analysis, the O_x (x = b or t) site behaves as an oxygen radical during the H abstraction, and the [Fe⁺-O_x^-] site behaves as a Lewis acid-base pair during the concerted C-H cleavage. Molecular orbital decomposition analysis further demonstrates electron transfer during the oxidation and reduction steps of the reaction. High-level multireference calculations were also carried out to further assess the DFT results. Understanding how these systems behave during the proposed reaction pathways provides new insights into how they can be tuned for methane partial oxidation.

Density-Functional Tight-Binding Study on the Effects of Interfacial Water in the Adhesion Force between Epoxy Resin and Alumina Surface

Adhesion is one of the most interesting subjects in interface phenomena from the viewpoint of wide-range applications as well as basic science. Interfacial water has significant effects on coatings, adhesives, and fiber-reinforced polymer composites, often causing adhesion loss. The way of thinking based on quantum mechanics is essential for a better understanding of physical and chemical properties of adhesive interfaces. In this work, the molecular mechanism of the adhesion interaction between epoxy resin and hydroxylated alumina surface in the presence of interfacial water molecules is investigated by using density-functional tight-binding calculations. Periodic slab model calculations demonstrate that hydrogen bond is an important factor at the adhesion interface. Effects of interfacial water molecules located between epoxy resin and hydroxylated alumina surface are assessed by using a dry model without interfacial water and wet models with water layers of 3, 6, and 9 Å thicknesses. Interesting first- and second-layer structures are observed in the distribution of interfacial water molecules in the tight space between the adhesive and adherend. Energy plots with respect to the displacement of epoxy resin from the alumina surface are nicely approximated by the Morse potential. The adhesion force and stress are theoretically obtained by differentiating the potential curve with respect to the displacement of epoxy resin. Computational results show that the adhesion force and stress are significantly weakened with an increase in the thickness of interfacial water layer. Thus, interfacial water molecules have a clue as to the role of water in the loss of adhesion.

Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools

This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations.

A DFT study on direct benzene hydroxylation catalyzed by framework Fe and Al sites in zeolites

Framework Fe rather than Al Lewis acidic sites in zeolites are demonstrated to show superior catalytic activity for benzene hydroxylation.

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.

Highly Selective Ferric Ion Sorption and Exchange by Crystalline Metal Phosphonates Constructed from Tetraphosphonic Acids

With the motivation of searching for highly selective ferric ion sorbents, two open-framework and microporous materials, {[Pb7(HEDTP)2(H2O)] x 7H2O}n (1) and {[Zn2(H4EDTP)] x 2H2O}n (2) [H8EDTP = N,N,N',N'-ethylenediaminetetrakis(methylenephosphonic acid)], have been synthesized and structurally characterized. The structure of compound 1 results from the seven crystallographically different lead atoms that are bridged by two HEDTP(7-) ligands to yield a three-dimensional microporous framework with tunnels along the a and b axes. Compound 2 features a layer architecture built of square waves along the a axis. The layers are connected by hydrogen bonds between uncoordinated phosphonate oxygen atoms to form a three-dimensional supramolecular network, with one-dimensional tunnels along the a axis. Both compounds 1 and 2 exhibited high ion sorption and exchange capacities for millimolar concentrations of Fe(III). Specifically, when 0.01 g of 1 (or 2) was added to 5 mL of a 1 mM metallic chloride aqueous solution and the mixture was allowed to stand for 2 days at room temperature, compound 1 adsorbed nearly 100% of Fe(III) and compound 2 adsorbed 96.8% of Fe(III). They were also found to adsorb ferric ions selectively over other metal ions, such as Ca(II), Cr(II), Mn(II), Cu(II), Zn(II), Cd(II), etc. Their special ferric ion uptake capacities may be attributed to the cation exchange, coordination bonding, and electrostatic attraction between ferric ions and metal phosphonates.