Selection and Validation of Charge and Lennard-Jones Parameters for QM/MM Simulations of Hydrocarbon Interactions with Zeolites

Tailoring parameters for QM/MM simulations: accurate modeling of adsorption and catalysis in zirconium-based metal-organic frameworks

Quantum mechanics/molecular mechanics (QM/MM) simulations offer an efficient way to model reactions occurring in complex environments. This study introduces a specialized set of charge and Lennard-Jones parameters tailored for electrostatically embedded QM/MM calculations, aiming to accurately model both adsorption processes and catalytic reactions in zirconium-based metal-organic frameworks (Zr-MOFs). To validate our approach, we compare adsorption energies derived from QM/MM simulations against experimental results and Monte Carlo simulation outcomes. The developed parameters showcase the ability of QM/MM simulations to represent long-range electrostatic and van der Waals interactions faithfully. This capability is evidenced by the prediction of adsorption energies with a low root mean square error of 1.1 kcal mol-1 across a wide range of adsorbates. The practical applicability of our QM/MM model is further illustrated through the study of glucose isomerization and epimerization reactions catalyzed by two structurally distinct Zr-MOF catalysts, UiO-66 and MOF-808. Our QM/MM calculations closely align with experimental activation energies. Importantly, the parameter set introduced here is compatible with the widely used universal force field (UFF). Moreover, we thoroughly explore how the size of the cluster model and the choice of density functional theory (DFT) methodologies influence the simulation outcomes. This work provides an accurate and computationally efficient framework for modeling complex catalytic reactions within Zr-MOFs, contributing valuable insights into their mechanistic behaviors and facilitating further advancements in this dynamic area of research.

Molecules in Environments: Toward Systematic Quantum Embedding of Electrons and Drude Oscillators

We develop a quantum embedding method that enables accurate and efficient treatment of interactions between molecules and an environment, while explicitly including many-body correlations. The molecule is composed of classical nuclei and quantum electrons, whereas the environment is modeled via charged quantum harmonic oscillators. We construct a general Hamiltonian and introduce a variational Ansatz for the correlated ground state of the fully interacting molecule-environment system. This wave function is optimized via the variational Monte Carlo method and the ground state energy is subsequently estimated through the diffusion Monte Carlo method. The proposed scheme allows an explicit many-body treatment of electrostatic, polarization, and dispersion interactions between the molecule and the environment. We study solvation energies and excitation energies of benzene derivatives, obtaining excellent agreement with explicit ab initio calculations and experiments.

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.

Assessing the stability of Pd-exchanged sites in zeolites with the aid of a high throughput quantum chemistry workflow

Cation exchanged-zeolites are functional materials with a wide range of applications from catalysis to sorbents. They present a challenge for computational studies using density functional theory due to the numerous possible active sites. From Al configuration, to placement of extra framework cation(s), to potentially different oxidation states of the cation, accounting for all these possibilities is not trivial. To make the number of calculations more tractable, most studies focus on a few active sites. We attempt to go beyond these limitations by implementing a workflow for a high throughput screening, designed to systematize the problem and exhaustively search for feasible active sites. We use Pd-exchanged CHA and BEA to illustrate the approach. After conducting thousands of explicit DFT calculations, we identify the sites most favorable for the Pd cation and discuss the results in detail. The high throughput screening identifies many energetically favorable sites that are non-trivial. Lastly, we employ these results to examine NO adsorption in Pd-exchanged CHA, which is a promising passive NOx adsorbent (PNA) during the cold start of automobiles. The results shed light on critical active sites for NOx capture that were not previously studied.

Cooling and diffusion characteristics of a hot carrier in the monolayer WS2

The characteristics of a hot carrier distributed in the C excitonic state of the monolayer WS₂ is investigated by exploiting the transient absorption (TA) spectroscopy. The hot carrier cooling lifetime gradually prolongs from 0.58 ps to 2.68 ps with the absorbed photon flux owing to the hot phonon bottleneck effect, as the excitation photon energy is 2.03 eV. Meanwhile, the normalized TA spectra shows that the spectral feature of hot carriers is different from that of normal carriers. Based on the modified Lennard-Jones model, the average distance among hot carriers can be estimated according to the peak shift of TA spectra and the diffusion velocity can also be calculated simultaneously. The hot carrier limits the diffusion of the photo-generated carrier at the initial several picoseconds. These results help people to elucidate the hot carrier dynamics in 2D TMDCs and give guidance on the designing and optimizing the TMDC-based electronic devices of high performance.

Computational Modeling Predicts the Stability of Both Pd+ and Pd2+ Ion-Exchanged into H-CHA

Passive NOx adsorbers (PNA) using Pd/zeolites have emerged as a promising solution for the reduction of cold-start emissions from vehicle exhaust. However, the nature of the active sites and the mechanisms underlying NOx adsorption in Pd/zeolites remain a subject of ongoing investigation. In this study, we employ quantum chemical simulations to investigate the structure of Pd species in cation-exchange sites at isolated Al and Al pairs in the 6-ring and 8-ring of the CHA framework, before the introduction of NOx. Our calculations show that the speciation of Pd in these exchange sites strongly depends on the precise Al arrangement within the framework, as well as the operating conditions. Ionically dispersed Pd is found to be the most favorable species over a wide range of oxidizing and reducing conditions. Small oligomers of PdO and metallic Pd do not appear to be competitive at either isolated Al or Al pairs. Notably, our calculations show that ion exchange sites other than next-next-nearest neighbor Al pairs in the 6-ring will be preferentially occupied by Pd+ instead of Pd2+. The stability of Pd+ in the zeolite environment is an interesting contrast with its rareness in molecular Pd compounds. Nonetheless, a detailed analysis of the electronic structure shows that predicted Pd oxidation states are consistent with chemical intuition for all complexes investigated in this study. We also discuss the potential ambiguity in Pd characterization provided by typical experimental techniques such as XANES, EXAFS and UV-VIS, and highlight the need for additional EPR spectroscopy studies to further elucidate the initial Pd speciation in zeolites for PNA applications.

Embedding Methods for Quantum Chemistry: Applications from Materials to Life Sciences

Quantum mechanical embedding methods hold the promise to transform not just the way calculations are performed, but to significantly reduce computational costs and improve scaling for macro-molecular systems containing hundreds if not thousands of atoms. The field of embedding has grown increasingly broad with many approaches of different intersecting flavors. In this perspective, we lay out the methods into two streams: QM:MM and QM:QM, showcasing the advantages and disadvantages of both. We provide a review of the literature, the underpinning theories including our contributions, and we highlight current applications with select examples spanning both materials and life sciences. We conclude with prospects and future outlook on embedding, and our view on the use of universal test case scenarios for cross-comparisons of the many available (and future) embedding theories.

Simulating protein-ligand binding with neural network potentials

Drug molecules adopt a range of conformations both in solution and in their protein-bound state. The strain and reduced flexibility of bound drugs can partially counter the intermolecular interactions that drive protein-ligand binding. To make accurate computational predictions of drug binding affinities, computational chemists have attempted to develop efficient empirical models of these interactions, although these methods are not always reliable. Machine learning has allowed the development of highly-accurate neural-network potentials (NNPs), which are capable of predicting the stability of molecular conformations with accuracy comparable to state-of-the-art quantum chemical calculations but at a billionth of the computational cost. Here, we demonstrate that these methods can be used to represent the intramolecular forces of protein-bound drugs within molecular dynamics simulations. These simulations are shown to be capable of predicting the protein-ligand binding pose and conformational component of the absolute Gibbs energy of binding for a set of drug molecules. Notably, the conformational energy for anti-cancer drug erlotinib binding to its target was found to be considerably overestimated by a molecular mechanical model, while the NNP predicts a more moderate value. Although the ANI-1ccX NNP was not trained to describe ionic molecules, reasonable binding poses are predicted for charged ligands, but this method is not suitable for modeling charged ligands in solution.

Mechanism and Kinetics of Propane Dehydrogenation and Cracking over Ga/H-MFI Prepared via Vapor-Phase Exchange of H-MFI with GaCl3

In this study, the mechanism and kinetics of C₃H₈ dehydrogenation and cracking are examined over Ga/H-MFI catalysts prepared via vapor-phase exchange of H-MFI with GaCl₃. The present study demonstrates that [GaH]²⁺ cations are the active centers for C₃H₈ dehydrogenation and cracking, independent of the Ga/Al ratio. For identical reaction conditions, [GaH]²⁺ cations in Ga/H-MFI exhibit a turnover frequency for C₃H₈ dehydrogenation that is 2 orders of magnitude higher and for C₃H₈ cracking, that is 1 order of magnitude higher than the corresponding turnover frequencies over H-MFI. C₃H₈ dehydrogenation and cracking exhibit first-order kinetics with respect to C₃H₈ over H-MFI, but both reactions exhibit first-order kinetics over Ga/H-MFI only at very low C₃H₈ partial pressures and zero-order kinetics at higher C₃H₈ partial pressures. H₂ inhibits both reactions over Ga/H-MFI. It is also found that the ratio of the rate of dehydrogenation to the rate of cracking over Ga/H-MFI is independent of C₃H₈ and H₂ partial pressures but weakly dependent on temperature. Measured activation enthalpies together with theoretical analysis are consistent with a mechanism in which both the dehydrogenation and cracking of C₃H₈ proceed over Ga/H-MFI via reversible, heterolytic dissociation of C₃H₈ at [GaH]²⁺ sites to form [C₃H₇-GaH]⁺-H⁺ cation pairs. The rate-determining step for dehydrogenation is the β-hydride elimination of C₃H₆ and H₂ from the C₃H₇ fragment. The rate-determining step for cracking is C-C bond attack of the same propyl fragment by the proximal Brønsted acid O-H group. H₂ inhibits both dehydrogenation and cracking over Ga/H-MFI via reaction with [GaH]²⁺ cations to form [GaH₂]⁺-H⁺ cation pairs.

Understanding Brønsted-Acid Catalyzed Monomolecular Reactions of Alkanes in Zeolite Pores by Combining Insights from Experiment and Theory

Acidic zeolites are effective catalysts for the cracking of large hydrocarbon molecules into lower molecular weight products required for transportation fuels. However, the ways in which the zeolite structure affects the catalytic activity at Brønsted protons are not fully understood. One way to characterize the influence of the zeolite structure on the catalysis is to study alkane cracking and dehydrogenation at very low conversion, conditions for which the kinetics are well defined. To understand the effects of zeolite structure on the measured rate coefficient (k_app ), it is necessary to identify the equilibrium constant for adsorption into the reactant state (K_ads-H+ ) and the intrinsic rate coefficient of the reaction (k_int ) at reaction temperatures, since k_app is proportional to the product of K_ads-H+ and k_int . We show that K_ads-H+ cannot be calculated from experimental adsorption data collected near ambient temperature, but can, however, be estimated accurately from configurational-bias Monte Carlo (CBMC) simulations. Using monomolecular cracking and dehydrogenation of C₃ -C₆ alkanes as an example, we review recent efforts aimed at elucidating the influence of the acid site location and the zeolite framework structure on the observed values of k_app and its components, K_ads-H+ and k_int .

Lewis Acid Zeolites for Biomass Conversion: Perspectives and Challenges on Reactivity, Synthesis, and Stability

Zeolites containing Sn, Ti, Zr, Hf, Nb, or Ta heteroatoms are versatile catalysts for the activation and conversion of oxygenated molecules owing to the unique Lewis acid character of their tetrahedral metal sites. Through fluoride-mediated synthesis, hydrophobic Lewis acid zeolites can behave as water-tolerant catalysts, which has resulted in a recent surge of experimental and computational studies in the field of biomass conversion. However, many open questions still surround these materials, especially relating to the nature of their active sites. This lack of fundamental understanding is exemplified by the many dissonant results that have been described in recent literature reports. In this review, we use a molecular-based approach to provide insight into the relationship between the structure of the metal center and its reactivity toward different substrates, with the ultimate goal of providing a robust framework to understand the properties that have the strongest influence on catalytic performance for the conversion of oxygenates.

CPMD/GULP QM/MM interface for modeling periodic solids: Implementation and its application in the study of Y-zeolite supported Rhn clusters

We report here the development of hybrid quantum mechanics/molecular mechanics (QM/MM) interface between the plane-wave density functional theory based CPMD code and the empirical force-field based GULP code for modeling periodic solids and surfaces. The hybrid QM/MM interface is based on the electrostatic coupling between QM and MM regions. The interface is designed for carrying out full relaxation of all the QM and MM atoms during geometry optimizations and molecular dynamics simulations, including the boundary atoms. Both Born-Oppenheimer and Car-Parrinello molecular dynamics schemes are enabled for the QM part during the QM/MM calculations. This interface has the advantage of parallelization of both the programs such that the QM and MM force evaluations can be carried out in parallel to model large systems. The interface program is first validated for total energy conservation and parallel scaling performance is benchmarked. Oxygen vacancy in α-cristobalite is then studied in detail and the results are compared with a fully QM calculation and experimental data. Subsequently, we use our implementation to investigate the structure of rhodium cluster (Rhn ; n = 2 to 6) formed from Rh(C2 H4 )2 complex adsorbed within a cavity of Y-zeolite in a reducible atmosphere of H2 gas. © 2016 Wiley Periodicals, Inc.

Adsorption in zeolites using mechanically embedded ONIOM clusters

We have explored mechanically embedded three-layer QM/QM/MM ONIOM models for computational studies of binding in Al-substituted zeolites.

Mechanism of alkane H/D exchange over zeolite H-ZSM-5 at low temperature: a combined computational and experimental study

Theoretical and experimental results have provided fundamental insights into the possible pathways for the H/D exchange of isobutane with H-ZSM-5 zeolite at room temperature.

A potential with low point charges for pure siliceous zeolites

A modified CHARMM force-field (ZHB potential) with low point charges for silica was previously proposed by Zimmerman et al. (J. Chem. Theory Comput. 2011, 7, 1695). The ZHB potential is advantageous for quantum mechanics/molecular mechanics simulations as it minimizes the electron spill-out problems. In the same spirit, here we propose a modified ZHB potential (MZHB) by reformulating its bonding potential, while retaining the nonbonding potential as in the ZHB force-field. We show that several structural and dynamic properties of silica, like the IR spectrum, distribution functions, mechanical properties, and negative thermal expansion computed using the MZHB potential agree well with experimental data. Further, transferability of MZHB is also tested for reproducing the crystallographic structures of several polymorphs of silica. © 2015 Wiley Periodicals, Inc.

Advances in theory and their application within the field of zeolite chemistry

Zeolites are versatile and fascinating materials which are vital for a wide range of industries, due to their unique structural and chemical properties, which are the basis of applications in gas separation, ion exchange and catalysis. Given their economic impact, there is a powerful incentive for smart design of new materials with enhanced functionalities to obtain the best material for a given application. Over the last decades, theoretical modeling has matured to a level that model guided design has become within reach. Major hurdles have been overcome to reach this point and almost all contemporary methods in computational materials chemistry are actively used in the field of modeling zeolite chemistry and applications. Integration of complementary modeling approaches is necessary to obtain reliable predictions and rationalizations from theory. A close synergy between experimentalists and theoreticians has led to a deep understanding of the complexity of the system at hand, but also allowed the identification of shortcomings in current theoretical approaches. Inspired by the importance of zeolite characterization which can now be performed at the single atom and single molecule level from experiment, computational spectroscopy has grown in importance in the last decade. In this review most of the currently available modeling tools are introduced and illustrated on the most challenging problems in zeolite science. Directions for future model developments will be given.

Molecular dynamics simulation of heterogeneous nucleation on nanotubes

Condensation rate inside and outside the tube depends on the pore diameter and length.