3 research outputs found
OGRe: Optimal Grid Refinement Protocol for Accurate Free Energy Surfaces and Its Application in Proton Hopping in Zeolites and 2D COF Stacking
While free energy surfaces are the crux of our understanding
of
many chemical and biological processes, their accuracy is generally
unknown. Moreover, many developments to improve their accuracy are
often complicated, limiting their general use. Luckily, several tools
and guidelines are already in place to identify these shortcomings,
but they are typically lacking in flexibility or fail to systematically
determine how to improve the accuracy of the free energy calculation.
To overcome these limitations, this work introduces OGRe, a Python
package for optimal grid refinement in an arbitrary number of dimensions.
OGRe is based on three metrics that gauge the confinement, consistency,
and overlap of each simulation in a series of umbrella sampling (US)
simulations, an enhanced sampling technique ubiquitously adopted to
construct free energy surfaces for hindered processes. As these three
metrics are fundamentally linked to the accuracy of the weighted histogram
analysis method adopted to generate free energy surfaces from US simulations,
they facilitate the systematic construction of accurate free energy
profiles, where each metric is driven by a specific umbrella parameter.
This allows for the derivation of a consistent and optimal collection
of umbrellas for each simulation, largely independent of the initial
values, thereby dramatically increasing the ease-of-use toward accurate
free energy surfaces. As such, OGRe is particularly suited to determine
complex free energy surfaces with large activation barriers and shallow
minima, which underpin many physical and chemical transformations
and hence to further our fundamental understanding of these processes
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-53Â(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 CO<sub>2</sub> and CH<sub>4</sub> 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 ÎĽ and mechanical pressure <i>P</i> as two independent thermodynamic variables and predict
the complete (ÎĽ, <i>P</i>) phase diagram for CO<sub>2</sub> adsorption in MIL-53Â(Cr). The free energy model proposed
here is an important step toward a general thermodynamics description
of flexible metal–organic frameworks
High-Throughput Screening of Covalent Organic Frameworks for Carbon Capture Using Machine Learning
Postcombustion carbon capture provides a high-potential
pathway
to reduce anthropogenic CO2 emissions in the short term.
In this respect, nanoporous materials, such as covalent organic frameworks
(COFs), offer a promising platform as adsorbent beds. However, due
to the modular nature of COFs, an almost unlimited number of structures
can possibly be synthesized. To efficiently identify promising materials
and reveal performance trends within the COF material space, we present
a computational high-throughput screening of 268,687 COFs for their
ability to efficiently and selectively separate CO2 from
the flue gas of power plants using a pressure swing adsorption process.
Furthermore, we demonstrate that our screening can be significantly
accelerated using machine learning to identify a set of promising
materials. These are subsequently characterized with high accuracy,
taking into account the effects of competitive adsorption and coadsorption.
Our screening reveals that imide, (keto)enamine, and (acyl)hydrazone
COFs are particularly interesting for carbon capture. Additionally,
the best-performing materials are 3D COFs possessing strong CO2 adsorption sites between aromatic rings at opposite sides
of pores with a diameter of 1.0 nm. In 2D COFs, a significant influence
of the framework chemistry, such as imide linkages or fluoro groups,
is observed. Our design rules can guide experimental researchers to
construct high-performing COFs for CO2 capture