Penilaian Karya Ilmiah C-11

Recent experimental work has shown that variations in the confinement of <i>n</i>-butane at Brønsted acid sites due to changes in zeolite framework structure strongly affect the apparent and intrinsic enthalpy and entropy of activation for cracking and dehydrogenation. Quantum chemical calculations have provided good estimates of the intrinsic enthalpies and entropies of activation extracted from experimental rate data for MFI, but extending these calculations to less confining zeolites has proven challenging, particularly for activation entropies. Herein, we report our efforts to develop a theoretical model for the cracking and dehydrogenation of <i>n</i>-butane occurring in a series of zeolites containing 10-ring channels and differing in cavity size (TON, FER, -SVR, MFI, MEL, STF, and MWW). We combine a QM/MM approach to calculate intrinsic and apparent activation parameters, with thermal corrections to the apparent barriers obtained from configurational-bias Monte Carlo simulations, to account for configurational contributions due to global motions of the transition state. We obtain good agreement between theory and experiment for all activation parameters for central cracking in all zeolites. For terminal cracking and dehydrogenation, good agreement between theory and experiment is found only at the highest confinements. Experimental activation parameters, especially those for dehydrogenation, tend to increase with decreasing confinement. This trend is not captured by the theoretical calculations, such that deviations between theory and experiment increase as confinement decreases. We propose that, because transition states for dehydrogenation are later than those for cracking, relative movements between the fragments produced in the reaction become increasingly important in the less confining zeolites

Reliably Modeling the Mechanical Stability of Rigid and Flexible Metal–Organic Frameworks

ConspectusOver the past two decades, metal–organic frameworks (MOFs) have matured from interesting academic peculiarities toward a continuously expanding class of hybrid, nanoporous materials tuned for targeted technological applications such as gas storage and heterogeneous catalysis. These oft-times crystalline materials, composed of inorganic moieties interconnected by organic ligands, can be endowed with desired structural and chemical features by judiciously functionalizing or substituting these building blocks. As a result of this reticular synthesis, MOF research is situated at the intriguing intersection between chemistry and physics, and the building block approach could pave the way toward the construction of an almost infinite number of possible crystalline structures, provided that they exhibit stability under the desired operational conditions. However, this enormous potential is largely untapped to date, as MOFs have not yet found a major breakthrough in technological applications. One of the remaining challenges for this scale-up is the densification of MOF powders, which is generally achieved by subjecting the material to a pressurization step. However, application of an external pressure may substantially alter the chemical and physical properties of the material. A reliable theoretical guidance that can presynthetically identify the most stable materials could help overcome this technological challenge.In this Account, we describe the recent research the progress on computational characterization of the mechanical stability of MOFs. So far, three complementary approaches have been proposed, focusing on different aspects of mechanical stability: (i) the Born stability criteria, (ii) the anisotropy in mechanical moduli such as the Young and shear moduli, and (iii) the pressure-versus-volume equations of state. As these three methods are grounded in distinct computational approaches, it is expected that their accuracy and efficiency will vary. To date, however, it is unclear which set of properties are suited and reliable for a given application, as a comprehensive comparison for a broad variety of MOFs is absent, impeding the widespread use of these theoretical frameworks.Herein, we fill this gap by critically assessing the performance of the three computational models on a broad set of MOFs that are representative for current applications. These materials encompass the mechanically rigid UiO-66­(Zr) and MOF-5­(Zn) as well as the flexible MIL-47­(V) and MIL-53­(Al), which undergo pressure-induced phase transitions. It is observed that the Born stability criteria and pressure-versus-volume equations of state give complementary insight into the macroscopic and microscopic origins of instability, respectively. However, interpretation of the Born stability criteria becomes increasingly difficult when less symmetric materials are considered. Moreover, pressure fluctuations during the simulations hamper their accuracy for flexible materials. In contrast, the pressure-versus-volume equations of state are determined in a thermodynamic ensemble specifically targeted to mitigate the effects of these instantaneous fluctuations, yielding more accurate results. The critical Account presented here paves the way toward a solid computational framework for an extensive presynthetic screening of MOFs to select those that are mechanically stable and can be postsynthetically densified before their use in targeted applications

High-Throughput Screening of Extrinsic Point Defect Properties in Si and Ge: Database and Applications

Increased computational resources now make it possible to generate large data sets solely from first principles. Such “high-throughput” screening is employed to create a database of embedding enthalpies for extrinsic point defects and their vacancy complexes in Si and Ge for 73 impurities from H to Rn. Calculations are performed both at the PBE and HSE06 levels of theory. The data set is verified by comparison of the predicted lowest-enthalpy positions with experimental observations. The effect of temperature on the relative occupation of defect sites is estimated through configurational entropy. Potential applications are demonstrated by selecting optimal vacancy traps, directly relevant to industrial processes such as Czochralski growth as a means to suppress void formation

High-Throughput Screening of Extrinsic Point Defect Properties in Si and Ge: Database and Applications

Increased computational resources now make it possible to generate large data sets solely from first principles. Such “high-throughput” screening is employed to create a database of embedding enthalpies for extrinsic point defects and their vacancy complexes in Si and Ge for 73 impurities from H to Rn. Calculations are performed both at the PBE and HSE06 levels of theory. The data set is verified by comparison of the predicted lowest-enthalpy positions with experimental observations. The effect of temperature on the relative occupation of defect sites is estimated through configurational entropy. Potential applications are demonstrated by selecting optimal vacancy traps, directly relevant to industrial processes such as Czochralski growth as a means to suppress void formation

Mechanical Properties from Periodic Plane Wave Quantum Mechanical Codes: The Challenge of the Flexible Nanoporous MIL-47(V) Framework

Modeling the flexibility of metal–organic frameworks (MOFs) requires the computation of mechanical properties from first principles, e.g., for screening of materials in a database, for gaining insight into structural transformations, and for force field development. However, this paper shows that computations with periodic density functional theory are challenged by the flexibility of these materials: guidelines from experience with standard solid-state calculations cannot be simply transferred to flexible porous frameworks. Our test case, the MIL-47­(V) material, has a large-pore and a narrow-pore shape. The effect of Pulay stress (cf. Pulay forces) leads to drastic errors for a simple structure optimization of the flexible MIL-47­(V) material. Pulay stress is an artificial stress that tends to lower the volume and is caused by the finite size of the plane wave basis set. We have investigated the importance of this Pulay stress, of symmetry breaking, and of <i>k</i>-point sampling on (a) the structure optimization and (b) mechanical properties such as elastic constants and bulk modulus, of both the large-pore and narrow-pore structure of MIL-47­(V). We found that, in the structure optimization, Pulay effects should be avoided by using a fitting procedure, in which an equation of state <i>E</i>(<i>V</i>) (EOS) is fit to a series of energy versus volume points. Manual symmetry breaking could successfully lower the energy of MIL-47­(V) by distorting the vanadium–oxide distances in the vanadyl chains and by rotating the benzene linkers. For the mechanical properties, the curvature of the EOS curve was compared with the Reuss bulk modulus, derived from the elastic tensor in the harmonic approximation. Errors induced by anharmonicity, the eggbox effect, and Pulay effects propagate into the Reuss modulus. The strong coupling of the unit cell axes when the unit cell deforms expresses itself in numerical instability of the Reuss modulus. For a flexible material, it is therefore advisible to resort to the EOS fit procedure

Critical Analysis of the Accuracy of Models Predicting or Extracting Liquid Structure Information

This work aims at a critical assessment of properties predicting or extracting information on the density and structure of liquids. State-of-the-art NVT and NpT molecular dynamics (MD) simulations have been performed on five liquids: methanol, chloroform, acetonitrile, tetrahydrofuran, and ethanol. These simulations allow the computation of properties based on first principles, including the equilibrium density and radial distribution functions (RDFs), characterizing the liquid structure. Refinements have been incorporated in the MD simulations by taking into account basis set superposition errors (BSSE). An extended BSSE model for an instantaneous evaluation of the BSSE corrections has been proposed, and their impact on the liquid properties has been assessed. If available, the theoretical RDFs have been compared with the experimentally derived RDFs. For some liquids, significant discrepancies have been observed, and a profound but critical investigation is presented to unravel the origin of these deficiencies. This discussion is focused on tetrahydrofuran where the experiment reveals some prominent peaks completely missing in any MD simulation. Experiments providing information on liquid structure consist mainly of neutron diffraction measurements offering total structure factors as the primary observables. The splitting of these factors in reciprocal space into intra- and intermolecular contributions is extensively discussed, together with their sensitivity in reproducing correct RDFs in coordinate space

On the Thermodynamics of Framework Breathing: A Free Energy Model for Gas Adsorption in MIL-53

When adsorbing guest molecules, the porous metal–organic framework MIL-53­(Cr) may vary its cell parameters drastically while retaining its crystallinity. A first approach to the thermodynamic analysis of this “framework breathing” consists of comparing the osmotic potential in two distinct shapes only (large-pore and narrow-pore). In this paper, we propose a generic parametrized free energy model including three contributions: host free energy, guest–guest interactions, and host–guest interaction. Free energy landscapes may now be constructed scanning all shapes and any adsorbed amount of guest molecules. This allows us to determine which shapes are the most stable states for arbitrary combinations of experimental control parameters, such as the adsorbing gas chemical potential, the external pressure, and the temperature. The new model correctly reproduces the structural transitions along the CO₂ and CH₄ isotherms. Moreover, our model successfully explains the adsorption versus desorption hysteresis as a consequence of the creation, stabilization, destabilization, and disappearance of a second free energy minimum under the assumptions of a first-order phase transition and collective behavior. Our general thermodynamic description allows us to decouple the gas chemical potential μ and mechanical pressure <i>P</i> as two independent thermodynamic variables and predict the complete (μ, <i>P</i>) phase diagram for CO₂ adsorption in MIL-53­(Cr). The free energy model proposed here is an important step toward a general thermodynamics description of flexible metal–organic frameworks

Molecular Dynamics Kinetic Study on the Zeolite-Catalyzed Benzene Methylation in ZSM‑5

The methylation of arenes is a key step in the production of hydrocarbons from methanol over acidic zeolites. We performed ab initio static and molecular dynamics free energy simulations of benzene methylation in H-ZSM-5 to determine the factors that influence the reaction kinetics. Special emphasis is given to the effect of the surrounding methanol molecules on the methylation kinetics. It is found that for higher methanol loadings, methylation may also occur from a protonated methanol cluster, indicating that the exact location of the Brønsted acid site is not essential for the zeolite-catalyzed methylation reaction. However, methylations from a protonated methanol cluster exhibit higher free energy barriers than a methylation from a single methanol molecule. Finally, comparison with a pure methanol solvent reaction environment indicates that the main role of the zeolite during the methylation of benzene is to provide the acidic proton and to create a polar environment for the reaction. The metadynamics approach, which is specifically designed to sample rare events, allows exploring new reaction pathways, which take into account the flexibility of the framework and additional guest molecules in the pores and channels of the zeolite framework. This approach goes beyond the often applied static calculations to determine reaction kinetics

Assessment of Atomic Charge Models for Gas-Phase Computations on Polypeptides

The concept of the atomic charge is extensively used to model the electrostatic properties of proteins. Atomic charges are not only the basis for the electrostatic energy term in biomolecular force fields but are also derived from quantum mechanical computations on protein fragments to get more insight into their electronic structure. Unfortunately there are many atomic charge schemes which lead to significantly different results, and it is not trivial to determine which scheme is most suitable for biomolecular studies. Therefore, we present an extensive methodological benchmark using a selection of atomic charge schemes [Mulliken, natural, restrained electrostatic potential, Hirshfeld-I, electronegativity equalization method (EEM), and split-charge equilibration (SQE)] applied to two sets of penta-alanine conformers. Our analysis clearly shows that Hirshfeld-I charges offer the best compromise between transferability (robustness with respect to conformational changes) and the ability to reproduce electrostatic properties of the penta-alanine. The benchmark also considers two charge equilibration models (EEM and SQE), which both clearly fail to describe the locally charged moieties in the zwitterionic form of penta-alanine. This issue is analyzed in detail because charge equilibration models are computationally much more attractive than the Hirshfeld-I scheme. Based on the latter analysis, a straightforward extension of the SQE model is proposed, SQE+Q⁰, that is suitable to describe biological systems bearing many locally charged functional groups

Tandem Addition of Phosphite Nucleophiles Across Unsaturated Nitrogen-Containing Systems: Mechanistic Insights on Regioselectivity

The addition of phosphite nucleophiles across linear unsaturated imines is a powerful and atom-economical methodology for the synthesis of aminophosphonates. These products are of interest from both a biological and a synthetic point of view: they act as amino acid transition state analogs and Horner–Wadsworth–Emmons reagents, respectively. In this work the reaction between dialkyl trimethylsilyl phosphites and <i>α,β,γ,δ</i>-diunsaturated imines was evaluated as a continuation of our previous efforts in the field. As such, the first conjugate 1,6-addition of a phosphite nucleophile across a linear unsaturated <i>N</i>-containing system is reported herein. Theoretical calculations were performed to rationalize the observed regioselectivites and to shed light on the proposed mechanism