Louis Vanduyfhuys

The extended adsorption information file format makes computational adsorption results easier to share and reuse. Vision-capable language models help recover literature isotherms for reporting in the same format.

ThermoLIB is a Python/Cython library designed to be used as a postprocessing tool for constructing free-energy surfaces, including adequate error estimation from the output of molecular simulations, transforming them between different collective variables (CVs), and extracting thermodynamic and kinetic information. ThermoLIB is available for download on GitHub and comes with extended documentation as well as many tutorials. The implementation is based on the theory of maximum-likelihood estimators for robust error estimation. The free-energy surfaces can be transformed or projected a posteriori to a larger or lower CV space by constructing conditional probabilities from the simulation results. Finally, useful CV-independent thermodynamic and kinetic properties, such as the rate constant, can be readily obtained, together with their uncertainty estimates. We briefly illustrate the capabilities of ThermoLIB by means of tutorials and case studies.

ThermoLIB is Python/Cython library designed to be used as a post-processing tool for constructing free energy surfaces from the output of molecular simulations, transforming them between different collective variables (CVs) and extracting thermodynamic and kinetic information. ThermoLIB is available for download on GitHUB and comes with extended documentation as well as many tutorials. The implementation is based on the theory of maximum likelihood estimators and includes error bars on and full covariance matrix between all points on the free energy surface using the Fisher information matrix. The free energy surfaces can be transformed a posteriori to other collective variables, projected towards lower dimensional CV-spaces and even deprojected towards higher dimensional CV-spaces if additional information from the simulation is provided in the form of a conditional probability. Finally, one can extract usefull thermodynamic and kinetic properties such as the reaction free energy and kinetic rate constant. Error bars on the free energy surfaces are propagated throughout al these operations. We briefly illustrate the capabilities of ThermoLIB by means of some tutorials and case studies.

A synergistic computational and experimental approach identified CAU-11(Al) as a top-performing adsorbent for selective acetone capture under humid conditions, combining high hydrophobicity and large acetone uptake at low concentrations.

An increasing number of ligand-bound membrane protein structures reveal ligand-binding sites on the lipid-exposed surface of the protein within the membrane bilayer. Binding events to such sites have previously been studied using molecular dynamics (MD) simulations and experiments in cases such as calcium-gated potassium channels ¹ and sodium channels ² . The proposed binding mechanism is that these ligands partition into the membrane to gain access to their binding site. What is currently unavailable is what the thermodynamic and kinetic contributions of the ligand-membrane and ligand-protein interactions are to the overall binding event. Here, we used MD simulations and enhanced sampling methods to study the membrane partitioning of a DHP calcium channel antagonist, nifedipine, from the voltage-gated calcium channel Cav1.1. We present that drug-membrane interactions occur on a much faster timescale than the overall binding of nifedipine to Cav1.1.

By tuning the steric environment and free pore space in metal-organic frameworks, a large variety of rotor dynamics of the organic linkers can appear. Nitrofunctionalized MIL-53 is a terephthalate-linker-based MOF that shows coupled rotor dynamics between the neighboring linkers along the pore direction. Here, we use classical molecular dynamics up to 6 × 2 × 2 supercells to investigate the range of the correlated linker dynamics. Interestingly, we observe an PNPNPNPN... conformational arrangement (P = nearly planar and N = nonplanar) for the conformations of the linkers in a row along the pore direction in the MOF. We identified correlated linker dynamics emerging among the direct and next nearest neighboring linkers along the pore. Due to 180° rotational flips of the planar linkers along the pore, (1) a change in the width of librations in their direct neighbors (PN) is observed; (2) intriguingly, their next nearest planar neighbors (PP) rotate between 0° and ±180° to reattain aligned (0°, 0°) or (±180°, ±180°) conformations. The presence of correlated dynamics in such linkers over long-length scales occurring at nanoseconds time scales is desirable for applications like ferroelectric switching or diffusion control via geared linker rotation, and this work provides insight into the design for such applications.

New lignocellulose biorefinery technologies that enable the conversion of lignin into platform chemicals are essential to reduce our future dependence on fossil resources. In this study, we investigate the Brønsted acid-catalyzed O-demethylation of guaiacol in hot-pressurized water (HPW) as a model reaction for transforming lignin-derived phenolic substrates featuring ortho methoxy groups. We compare the effects of Brønsted mineral acid (HCl) and microporous solid acid (H-BEA zeolite) in water to elucidate the hydrolysis mechanism and the impact of zeolite microporosity on reaction rates. Operando molecular modeling combined with experimental kinetic studies reveals that, regardless of the catalyst type, O-demethylation follows a concerted, one-step O-activated SN2 mechanism. This mechanism involves a strong hydrogen bond between guaiacol and a hydronium ion as an ionic contact pair. Protons confined within the zeolite form more active undercoordinated hydronium ions, which are associated with lower enthalpic requirements and thus accelerate the hydrolysis. The molecular organization of solvent and reactants around the confined catalytic active site plays a crucial role in modulating the association of the reacting species. These proof-of-concept results demonstrate the significant influence of solvent (water) coordination on acid-catalyzed bimolecular reactions, such as hydrolysis, within confined spaces.