1,721,031 research outputs found
Effect of anharmonicity on adsorption thermodynamics
Full text linkThe effect of anharmonic corrections to the vibrational energies of extended systems is explored. Particular attention is paid to the thermodynamics of adsorption of small molecules on catalytically relevant systems typically affected by anharmonicity. The implemented scheme obtains one-dimensional anharmonic model potentials by distorting the equilibrium structure along the normal modes using both rectilinear (Cartesian) or curvilinear (internal) representations. Only in the latter case, the modes are decoupled also at higher order of the potential and the thermodynamic functions change in the expected directions. The method is applied to calculate ab initio enthalpies, entropies, and Gibbs free energies for the adsorption of methane in acidic chabazite (H-CHA) and on MgO(001) surface. The values obtained for the adsorption of methane in H-CHA (273.15 K, 0.1 MPa, θ = 0.5) are ΔH = -19.3, -TΔS = 11.9, and ΔG = -7.5 kJ/mol. For methane on the MgO(001) (47 K, 1.3 × 10-14 MPa, θ = 1) ΔH = -14.4, -TΔS = 16.6, and ΔG = 2.1 kJ/mol are obtained. The calculated desorption temperature is 44 K, and the desorption prefactor is 4.26 × 10 12 s-1. All calculated results agree within chemical accuracy limits with experimental data. © 2014 American Chemical Society
FESTA: A Polygon-Based Approach for Extracting Relevant Structures from Free Energy Surfaces Obtained in Molecular Simulations
No full textAn easy-to-use script named FESTA (Free Energy Surface Trajectory Analysis) is provided to streamline the extraction of equilibrium structures from free energy maps obtained with enhanced sampling simulation techniques and their associated trajectories. This approach efficiently identifies relevant structures by automatically selecting minima on the free energy surface using a connected-component labeling algorithm and extracts them utilizing a Shapely-polygon-based trajectory analysis process. The script is general and portable; it incorporates an automatic periodicity detection system; and multiprocessing is utilized to leverage all available computational resources for enhanced efficiency. The effectiveness of the proposed polygon-based approach is demonstrated through comparison with a naïve and largely inefficient loop-based script and its application across three distinct systems for benchmarking purposes
Accurate Quantum Chemical Free Energies at Affordable Cost
No full textFree energy sampling methods allow studying the full dynamics of activated processes. Unfortunately, the affordable accuracy of the potential describing the energy and forces of the system is usually rather low. Here we introduce a new method that by combining metadynamics and free energy perturbation allows calculating accurate quantum chemical free energies for chemical reactions. To prove the effectiveness of this new approach we study the SN2 reaction of CH3F + Cl- → CH3Cl + F- in vacuo and solvated by water. Comparisons are made with harmonic transition-state theory to show how this method could provide accurate equilibrium and rate constants for complex systems
Enantioselective Tail-to-Head Terpene Cyclizations by Optically Active Hexameric Resorcin[4]arene Capsule Derivatives
Full text linkMolecular capsules enable the conversion of substrates inside a closed cavity, mimicking to some extent enzymatic catalysis. Chirality transfer from the molecular capsule onto the encapsulated substrate has been only studied in a few cases. Here we demonstrate that chirality transfer is possible inside a rather large molecular container of approximately 1400 Å3. Specifically, we present 1) the first examples of optically active hexameric resorcin[4]arene capsules, 2) their ability to enantioselectively catalyze tail-to-head terpene cyclizations, and 3) the surprisingly high sensitivity of enantioselectivity on the structural modifications
Fluoxetine vs Amitriptyline in the treatment of Anxious-Agitated Major Depression: a multicenter double blind study
No full textSupramolecular Capsule-Catalyzed Highly β-Selective Furanosylation Independent of the SN1/SN2 Reaction Pathway
No full textThe resorcin[4]arene capsule was found to catalyze β-selective furanosylation reactions for a variety of different furanosyl donors: α-d- and α-l-arabinosyl-, α-l-fucosyl-, α-d-ribosyl-, α-d-xylosyl-, and even α-d-lyxosyl fluorides. The scope is only limited by the inherently finite volume inside the closed capsular catalyst. The catalyst is readily available on a multi-100 g scale and can be recycled for at least seven rounds without significant loss in activity, yield, and selectivity. The mechanistic investigations indicated that the furanosylation mechanism is shifted toward an SN1 reaction on the mechanistic continuum between the prototypical SN1 and SN2 substitution types, as compared to the pyranosylation reaction inside the same catalyst. This is especially true for the lyxosyl donor, as indicated by the nucleophile reaction order of 0.26, and supported by metadynamics calculations. The mechanistic shift toward SN1 is of high interest as it indicates that this catalyst not only enables β-selective furanosylations and pyranoslyations independently of the substrate configuration but in addition also independently of the operating mechanism. To our knowledge, there is no alternative catalyst available that displays such properties
Deep learning the slow modes for rare events sampling
No full textThe development of enhanced sampling methods has greatly extended the scope of atomistic simulations, allowing longtime phenomena to be studied with accessible computational resources. Many such methods rely on the identification of an appropriate set of collective variables. These are meant to describe the system's modes that most slowly approach equilibrium under the action of the sampling algorithm. Once identified, the equilibration of these modes is accelerated by the enhanced sampling method of choice. An attractive way of determining the collective variables is to relate them to the eigenfunctions and eigenvalues of the transfer operator. Unfortunately, this requires knowing the long-term dynamics of the system beforehand, which is generally not available. However, we have recently shown that it is indeed possible to determine efficient collective variables starting from biased simulations. In this paper, we bring the power of machine learning and the efficiency of the recently developed on the fly probability-enhanced sampling method to bear on this approach. The result is a powerful and robust algorithm that, given an initial enhanced sampling simulation performed with trial collective variables or generalized ensembles, extracts transfer operator eigenfunctions using a neural network ansatz and then accelerates them to promote sampling of rare events. To illustrate the generality of this approach, we apply it to several systems, ranging from the conformational transition of a small molecule to the folding of aminiprotein and the study of materials crystallization
Ab initio study of methanol and ethanol adsorption on Brønsted sites in zeolite H-MFI
No full textWe examine the interaction of methanol and ethanol with a bridging OH group of H-MFI (Al12-O20(H)-Si3 site). The computational standard approach for molecule-surface interaction uses density functional theory with inclusion of dispersion for energies and harmonic vibrational frequencies for entropies and finite temperature effects for enthalpies. At 300 K, this yields -117 and -135 kJ mol-1 for adsorption enthalpies of methanol and ethanol, respectively, and 59 and 61 kJ mol-1, respectively for their entropy terms -T·ΔS. To reach chemical accuracy (±4 kJ mol-1) we go beyond this approach. The energies are calculated using a hybrid QM:QM scheme (QM-quantum mechanics) which combines plane-wave density functional theory accounting for the periodicity of the system with wave function-based methods (Møller-Plesset perturbation and Coupled Cluster theories). Finite temperature and entropy contributions are calculated from anharmonic vibrational partition functions. This yields as final predictions for methanol and ethanol -84 and -104 kJ mol-1, respectively, for the enthalpies of adsorption, 56 and 48 kJ mol-1, respectively, for the -T·ΔS term, and -28 and -56 kJ mol-1, respectively, for the Gibbs free energies at 300 K
Ab-Initio Calculation of Rate Constants for Molecule-Surface Reactions with Chemical Accuracy
Full text linkThe ab initio prediction of reaction rate constants for systems with hundreds of atoms with an accuracy that is comparable to experiment is a challenge for computational quantum chemistry. We present a divide-and-conquer strategy that departs from the potential energy surfaces obtained by standard density functional theory with inclusion of dispersion. The energies of the reactant and transition structures are refined by wavefunction-type calculations for the reaction site. Thermal effects and entropies are calculated from vibrational partition functions, and the anharmonic frequencies are calculated separately for each vibrational mode. This method is applied to a key reaction of an industrially relevant catalytic process, the methylation of small alkenes over zeolites. The calculated reaction rate constants (free energies), pre-exponential factors (entropies), and enthalpy barriers show that our computational strategy yields results that agree with experiment within chemical accuracy limits (less than one order of magnitude). A new strategy enables accurate quantum-mechanical ab initio predictions for the methylation of small alkenes over zeolite catalysts. The calculated reaction rate constants (free energies), pre-exponential factors (entropies), and enthalpy barriers show that this computational strategy yields results that agree with experiment within chemical accuracy limits
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