Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics

The methanol‐to‐olefin process is a showcase example of complex zeolite‐catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first principle molecular dynamics techniques to capture this complexity is shown by means of two case studies. Firstly, the adsorption behavior of methanol and water in H‐SAPO‐34 at 350 °C is investigated. Hereby an important degree of framework flexibility and proton mobility was observed. Secondly, the methylation of benzene by methanol through a competitive direct and stepwise pathway in the AFI topology was studied. Both case studies clearly show that a first‐principle molecular dynamics approach enables unprecedented insights into zeolite‐catalyzed reactions at the nanometer scale to be obtained.     

Local structure and thermodynamics of a core-softened potential fluid: theory and simulation.

Phase behavior and structural properties of homogeneous and inhomogeneous core-softened (CS) fluid consisting of particles interacting via the potential, which combines the hard-core repulsion and double attractive well interaction, are investigated. The vapour-liquid coexistence curves and critical points for various interaction ranges of the potential are determined by discrete molecular dynamics simulations to provide guidance for the choice of the bulk density and potential parameters for the study of homogeneous and inhomogeneous structures. Spatial correlations in the homogeneous CS system are studied by the Ornstein-Zernike integral equation in combination with the modified hypernetted chain (MHNC) approximation. The local structure of CS fluid subjected to diverse external fields maintaining the equilibrium with the bulk CS fluid are studied on the basis of a recently proposed third order+second order perturbation density functional approximation (DFA). The accuracy of DFA predictions is tested against the results of a grand canonical ensemble Monte Carlo simulation. Reasonable agreement between the results of both methods proves that the DFA theory applied in this work is a convenient theoretical tool for the investigation of the CS fluid, which is practically applicable for modeling numerous real systems.     

Spectroscopic Signature of Dynamical Instability of the Aqueous Complex in the Brown-Ring Nitrate Test**

The chemistry of the brown-ring test has been investigated for nearly a century. Though recent studies have focused on solid state structure determination and measurement of spectra, mechanistic details and kinetics, the aspects of solution structure and dynamics remain unknown. We have studied structural fluctuations of the brown-ring complex in aqueous solution with ab-initio molecular dynamics simulations, from which we identified that the classically established pseudo-octahedral [Fe(H₂O)₅(NO)]²⁺ complex is present along with a square-pyramidal [Fe(H₂O)₄(NO)]²⁺ complex. Based on the inability in multi-reference calculations to reproduce the experimental UV-vis spectra in aqueous solution by inclusion of thermal fluctuations of the [Fe(H₂O)₅(NO)]²⁺ complex alone, we propose the existence of an equilibrium between pseudo-octahedral and square-pyramidal complexes. Despite challenges in constructing models reproducing the solid-state UV-vis spectrum, the advanced spectrum simulation tool motivates us to challenge the established picture of a sole pseudo-octahedral complex in solution.     

How Water and Ion Mobility Affect the NMR Fingerprints of the Hydrated JBW Zeolite: A Combined Computational-Experimental Investigation

An important aspect within zeolite synthesis is to make fully tunable framework materials with controlled aluminium distribution. A major challenge in characterising these zeolites at operating conditions is the presence of water. In this work, we investigate the effect of hydration on the ²⁷Al NMR parameters of the ultracrystalline K,Na-compensated aluminosilicate JBW zeolite using experimental and computational techniques. The JBW framework, with Si/Al ratio of 1, is an ideal benchmark system as a stepping stone towards more complicated zeolites. The presence and mobility of water and extraframework species directly affect NMR fingerprints. Excellent agreement between theoretical and experimental spectra is obtained provided dynamic methods are employed with hydrated structural models. This work shows how NMR is instrumental in characterising aluminium distributions in zeolites at operating conditions.     

Predicting Inclusion Behaviour and Framework Structures in Organic Crystals

We have used well‐established computational methods to generate and explore the crystal structure landscapes of four organic molecules of well‐known inclusion behaviour. Using these methods, we are able to generate both close‐packed crystal structures and high‐energy open frameworks containing voids of molecular dimensions. Some of these high‐energy open frameworks correspond to real structures observed experimentally when the appropriate guest molecules are present during crystallisation. We propose a combination of crystal structure prediction methodologies with structure rankings based on relative lattice energy and solvent‐accessible volume as a way of selecting likely inclusion frameworks completely ab initio. This methodology can be used as part of a rational strategy in the design of inclusion compounds, and also for the anticipation of inclusion behaviour in organic molecules.     

Understanding the Role of Water in Aqueous Ruthenium‐Catalyzed Transfer Hydrogenation of Ketones.

We report an accurate computational study of the role of water in transfer hydrogenation of formaldehyde with a ruthenium‐based catalyst using a water‐specific model. Our results suggest that the reaction mechanism in aqueous solution is significantly different from that in the gas phase or in methanol solution. Previous theoretical studies have shown a concerted hydride and proton transfer in the gas phase (M. Yamakawa, H. Ito, R. Noyori, J. Am. Chem. Soc. 2000 , 122, 1466–1478;J.‐W. Handgraaf, J. N. H. Reek, E. J. Meijer, Organometallics 2003 , 22, 3150–3157; D. A. Alonso, P. Brandt, S. J. M. Nordin, P. G. Andersson, J. Am. Chem. Soc. 1999 , 121, 9580–9588; D. G. I. Petra, J. N. H. Reek, J.‐W. Handgraaf, E. J. Meijer, P. Dierkes, P. C. J. Kamer, J. Brussee, H. E. Schoemaker, P. W. N. M. van Leeuwen, Chem. Eur. J. 2000 , 6, 2818–2829), whereas a delayed, solvent‐mediated proton transfer has been observed in methanol solution (J.‐W. Handgraaf, E. J. Meijer, J. Am. Chem. Soc. 2007 , 129, 3099–3103). In aqueous solution, a concerted transition state is observed, as in the previous studies. However, only the hydride is transferred at that point, whereas the proton is transferred later by a water molecule instead of the catalyst.     

Organic Spacers in 2D Perovskites: General Trends and Structure-Property Relationships from Computational Studies

Addition of large organic molecules to halide perovskites has been shown to provoke dimensionality reduction and formation of two-dimensional phases that demonstrate improved long-term stabilities. Optoelectronic properties of the resulting 2D layered perovskites are strongly influenced by the chemical nature of the additive molecules, which opens immense possibilities for preparation of materials with tailored properties. However, given the huge chemical space of possible organic spacers, a systematic and exhaustive search for optimal compounds is impossible and general structure–property relationships that could guide a rational design are still largely absent. Here, we provide an overview of a series of recent computational studies from our group on different types of spacers. We first develop a simplified universal monovalent cation model to map out approximate structural stability maps as a function of the van der Waals radius and the magnitude of dispersion interactions to monitor the possible emergence of 2D phases. We further provide structural and photophysical insights from classical and first-principles molecular dynamics simulations and density functional theory calculations on 2D hybrid perovskites based on a wide range of spacers with different chemical nature and varying conformational properties. Our computational predictions are validated through comparison with powder diffraction, conductivity and optical measurements. Such comparative study allows for providing some general structure–property correlations, which can serve as design guidelines in the search for optimal 2D and mixed 2D/3D perovskite photovoltaic materials.     

Binding of Cationic and Neutral Phenanthridine Intercalators to a DNA Oligomer Is Controlled by Dispersion Energy: Quantum Chemical Calculations and Molecular Mechanics Simulations

Correlated ab initio as well as semiempirical quantum chemical calculations and molecular dynamics simulations were used to study the intercalation of cationic ethidium, cationic 5‐ethyl‐6‐phenylphenanthridinium and uncharged 3,8‐diamino‐6‐phenylphenanthridine to DNA. The stabilization energy of the cationic intercalators is considerably larger than that of the uncharged one. The dominant energy contribution with all intercalators is represented by dispersion energy. In the case of the cationic intercalators, the electrostatic and charge‐transfer terms are also important. The ΔG of ethidium intercalation to DNA was estimated at ?4.5 kcal mol^?1 and this value agrees well with the experimental result. Of six contributions to the final free energy, the interaction energy value is crucial. The intercalation process is governed by the non‐covalent stacking (including charge‐transfer) interaction while the hydrogen bonding between the ethidium amino groups and the DNA backbone is less important. This is confirmed by the evaluation of the interaction energy as well as by the calculation of the free energy change. The intercalation affects the macroscopic properties of DNA in terms of its flexibility. This explains the easier entry of another intercalator molecule in the vicinity of an existing intercalation site.     

On the quantum nature of an excess proton in liquid hydrogen fluoride.

Liquid hydrogen fluoride consists of chains of hydrogen-bonded molecules. The nature of an excess proton in liquid HF, which is of interest not only for its own sake, but also in relation to super-acid chemistry and to its behavior in water, has been studied using computer simulations. The methodology employed is the density-functional-theory-based path-integral Car-Parrinello ab initio molecular dynamics. The excess proton, which formally exists as a H2F+ or a H2F2+ defect in an HF chain, is found to strongly perturb the chain to which it is attached. Moreover, due to large zero-point energy, the charge defect is largely delocalized over several HF molecules.     

The Molecular Structure of gauche‐1,3‐Butadiene: Experimental Establishment of Non‐planarity

The planarity of the second stable conformer of 1,3‐butadiene, the archetypal diene for the Diels–Alder reaction in which a planar conjugated diene and a dienophile combine to form a ring, is not established. The most recent high level calculations predicted the species to adopt a twisted, gauche structure owing to steric interactions between the inner terminal hydrogens rather than a planar, cis structure favored by the conjugation of the double bonds. The structure cis‐1,3‐butadiene is unambiguously confirmed experimentally to indeed be gauche with a substantial dihedral angle of 34°, in excellent agreement with theory. Observation of two tunneling components indicates that the molecule undergoes facile interconversion between two equivalent enantiomeric forms. Comparison of experimentally determined structures for gauche‐ and trans‐butadiene provides an opportunity to examine the effects of conjugation and steric interactions.     

Experimental and Theoretical Study of the Ultrafast Dynamics of a Ni2Dy2-Compound in DMF After UV/Vis Photoexcitation

We present a combined experimental and theoretical study of the ultrafast transient absorption spectroscopy results of a {Ni₂Dy₂}-compound in DMF, which can be considered as a prototypic molecule for single molecule magnets. We apply state-of-the-art ab initio quantum chemistry to quantitatively describe the optical properties of an inorganic complex system comprising ten atoms to form the chromophoric unit, which is further stabilized by surrounding ligands. Two different basis sets are used for the calculations to specifically identify two dominant peaks in the ground state. Furthermore, we theoretically propagate the compound's correlated many-body wavefunction under the influence of a laser pulse as well as relaxation processes and compare against the time-resolved absorption spectra. The experimental data can be described with a time constant of several hundreds of femtoseconds attributed to vibrational relaxation and trapping into states localized within the band gap. A second time constant is ascribed to the excited state while trap states show lifetimes on a longer timescale. The theoretical propagation is performed with the density-matrix formalism and the Lindblad superoperator, which couples the system to a thermal bath, allowing us to extract relaxation times from first principles.     

First principles and experimental 1H NMR signatures of solvated ions: The case of HCl(aq).

A combined experimental and ab initio study is presented of the 1H NMR chemical shift distribution of aqueous hydrogen chloride solution as a function of acid concentration, based on Car-Parrinello molecular dynamics simulations and fully periodic NMR chemical-shift calculations. The agreement of computed and experimental spectra is very good. From first-principles calculations, we can show that the individual contributions of Eigen and Zundel ions, regular water molecules, and the chlorine solvation shell to the NMR line are very distinct and almost independent of the acid concentration. From the computed instantaneous NMR distributions, it is further possible to characterize the average variation in hydrogen-bond strength of the different complexes.     

Ferric and ferrous iron in nitroso-myoglobin: computer simulations of stable and metastable States and their infrared spectra.

The binding of NO to iron is involved in the biological function of many heme proteins. Contrary to ligands like CO and O(2), which only bind to ferrous (Fe(II)) iron, NO binds to both ferrous and ferric (Fe(III)) iron. In a particular protein, the natural oxidation state can therefore be expected to be tailored to the required function. Herein, we present an ab initio potential-energy surface for ferric iron interacting with NO. This potential-energy surface exhibits three minima corresponding to eta(1)-NO coordination (the global minimum), eta(1)-ON coordination and eta(2) coordination. This contrasts with the potential-energy surface for Fe(II)-NO, which exhibits only two minima (the eta(2) coordination mode for Fe(II) is a transition state, not a minimum). In addition, the binding energies of NO are substantially larger for Fe(III) than for Fe(II). We have performed molecular dynamics simulations for NO bound to ferric myoglobin (Mb(III)) and compare these with results obtained for Mb(II). Over the duration of our simulations (1.5 ns), all three binding modes are found to be stable at 200 K and transiently stable at 300 K, with eventual transformation to the eta(1)-NO global-minimum conformation. We discuss the implication of these results related to studies of rebinding processes in myoglobin.     

The Role of Packing,Dispersion, Electrostatics,and Solvation in High-Affinity Complexes of Cucurbit[n]urils with Uncharged Polar Guests

The rationalization of non-covalent binding trends is both of fundamental interest and provides new design concepts for biomimetic molecular systems. Cucurbit[n]urils (CBn) are known for a long time as the strongest synthetic binders for a wide range of (bio)organic compounds in water. However, their host-guest binding mechanism remains ambiguous despite their symmetric and simple macrocyclic structure and the wealth of literature reports. We herein report experimental thermodynamic binding parameters (ΔG, ΔH, TΔS) for CB7 and CB8 with a set of hydroxylated adamantanes, di-, and triamantanes as uncharged, rigid, and spherical/ellipsoidal guests. Binding geometries and binding energy decomposition were obtained from high-level theory computations. This study reveals that neither London dispersion interactions, nor electronic energies or entropic factors are decisive, selectivity-controlling factors for CBn complexes. In contrast, peculiar host-related solvation effects were identified as the major factor for rationalizing the unique behavior and record-affinity characteristics of cucurbit[n]urils.     

Ab initio Study of the Interactions between CO2 and N‐Containing Organic Heterocycles

In the garden of dispersion: High‐accuracy ab initio calculations are performed to determine the nature of the interactions and the most favorable geometries between CO₂ and heteroaromatic molecules containing nitrogen (see figure). Dispersion forces play a key role in the stabilization of the dimer, because correlation effects represent about 50 % of the total interaction energy.

     

The mechanism of formamide hydrolysis in water from ab initio calculations and simulations

The neutral hydrolysis of formamide in water is a suitable reference to quantify the efficiency of proteolytic enzymes. However, experimental data for this reaction has only very recently been obtained and the kinetic constant determined experimentally is significantly higher than that predicted by previous theoretical estimations. In this work, we have investigated in detail the possible mechanisms of this reaction. Several solvent models have been considered that represent a considerable improvement on those used in previous studies. Density functional and ab initio calculations have been carried out on a system which explicitly includes the first solvation shell of the formamide molecule. Its interaction with the bulk has been treated with the aid of a dielectric continuum model. Molecular dynamics simulations at the combined density functional/molecular mechanics level have been carried out in parallel to better understand the structure of the reaction intermediates in aqueous solution. Overall, the most favored mechanism predicted by our study involves two reaction steps. In the first step, the carbonyl group of the formamide molecule is hydrated to form a diol intermediate. The corresponding transition structure involves two water molecules. From this intermediate, a water-assisted proton transfer occurs from one of the hydroxy groups to the amino group. This reaction step may lead either to the formation of a new reaction intermediate with a marked zwitterionic character or to dissociation of the system into ammonia and formic acid. The zwitterionic intermediate dissociates quite easily but its lifetime is not negligible and it could play a role in the hydrolysis of substituted amides or peptides. The predicted pseudo-first-order kinetic constant for the rate-limiting step (the first step) of the hydrolysis reaction at 25 degrees C (3.9x10(-10) s(-1)) is in excellent agreement with experimental data (1.1x10(-10) s(-1)).     

Defect Dynamics in MAPbI3 Polycrystalline Films: The Trapping Effect of Grain Boundaries

Metal halide perovskites, chemical compounds of ABX₃ stoichiometry (A=CH₃NH₃⁺, Cs⁺, …; B=Pb²⁺, Sn²⁺; X=I⁻, Br⁻), have attracted great interest as they emerged as one of the most promising class of materials for low-cost photovoltaics with over 25 % certified power conversion efficiency. An important open question for further improving their efficiency and stability is the formation and dynamics of point defects, for example, iodide vacancies and interstitials. In particular, recently it has been shown that defects strongly interact with grain boundaries, which, for example, prevents a quick restoration of initial conditions of film when kept in the dark after illumination [Phung et al., Adv. Energy Mater. 2020 , 1903735]. It has also been shown that iodide defects may accumulate at grain boundaries, where they induce carriers’ recombination [Park et al., ACS Energy Lett. 2019 , 4, 1321–1327]. In this article, we make use of molecular dynamics and ab initio simulations to follow the evolution and compute the energetics of a iodide vacancy, , and an iodide Interstitial, , interacting with Σ5/(102) grain boundaries of different termination, MAI and PbI₂. We show that the polarization charge of Σ5/(102) grain boundary associated to a prescribed termination drives the dynamics of charged defects, and . The long-range interaction of grain boundaries with charged species might induce the accumulation of point defects present in crystallites or formed under operation conditions. Moreover, the selective attraction of specific defects by a grain boundary may help splitting Frenkel pairs formed in solar cells under illumination, thus preventing the quick annihilation of defects and enhancing the effect of light in inducing degradation processes.     

Global versus Local Aromaticity in Porphyrinoid Macrocycles: Experimental and Theoretical Study of “Imidacene”, an Imidazole‐Containing Analogue of Porphycene

The synthesis, spectroscopic properties, and computational analysis of an imidazole‐based analogue of porphycene are described. The macrocycle, given the trivial name “imidacene”, was prepared by reductive coupling of a diformyl‐substituted 2,2′‐biimidazole using low‐valent titanium, followed by treatment with 2,3‐dichloro‐5,6‐dicyano‐1,4‐benzoquinone. Imidacene displays a porphyrin‐like electronic structure, as judged by its ¹H NMR, ¹³C NMR, and UV/Vis spectral characteristics. Despite a cyclic 18 π‐electron pathway, dichloromethane or ethyl acetate solutions of imidacene were found to undergo rapid decomposition, even in the absence of light and air. A series of high‐level theoretical calculations, performed to probe the origin of this instability, revealed that the presence of a delocalized 18 π‐electron pathway in both imidacene and porphycene provides less aromatic stabilization energy than locally aromatic 6 π‐electron heterocycles in their reduced counterparts. That reduction of imidacene occurs on perimeter nitrogen atoms allows it to maintain its planarity and two stabilizing intramolecular hydrogen bonds, thereby distinguishing it from porphycene and, more generally, from porphyrin. Despite the presence of both 18 π‐ and 22 π‐electron pathways in the planar, reduced form of imidacene, aromaticity is evident only in the 6 π‐electron five‐membered rings. Our computational analysis predicts that routine ¹H NMR spectroscopy can be used to distinguish between local and global aromaticity in planar porphyrinoid macrocycles; the difference in the chemical shift for the internal NH protons is expected to be on the order of 19 ppm for these two electronically disparate sets of ostensibly similar compounds.