Rapid screening of nanopore candidates in nanoporous single-layer graphene for selective separations using molecular visualization and interatomic potentials

Abstract

Nanoporous single-layer graphene is promising as an ideal membrane because of its extreme thinness, chemical resistance, and mechanical strength, provided that selective nanopores are successfully incorporated. However, screening and understanding the transport characteristics of the large number of possible pores in graphene are limited by the high computational requirements of molecular dynamics (MD) simulations and the difficulty in experimentally characterizing pores of known structures. MD simulations cannot readily simulate the large number of pores that are encountered in actual membranes to predict transport, and given the huge variety of possible pores, it is hard to narrow down which pores to simulate. Here, we report alternative routes to rapidly screen molecules and nanopores with negligible computational requirement to shortlist selective nanopore candidates. Through the 3D representation and visualization of the pores’ and molecules’ atoms with their van der Waals radii using open-source software, we could identify suitable C-passivated nanopores for both gas- and liquid-phase separation while accounting for the pore and molecule shapes. The method was validated by simulations reported in the literature and was applied to study the mass transport behavior across a given distribution of nanopores. We also designed a second method that accounts for Lennard-Jones and electrostatic interactions between atoms to screen selective non-C-passivated nanopores for gas separations. Overall, these visualization methods can reduce the computational requirements for pore screening and speed up selective pore identification for subsequent detailed MD simulations and guide the experimental design and interpretation of transport measurements in nanoporous atomically thin membranes.

Ion Density-Dependent Dynamic Conductance Switching in Biomimetic Graphene Nanopores

“…Due to the rapid development of nanofabrication, the manufacturing precision of synthetic nanofluidic devices is approaching a single-nanometer scale or even the subnanometer regime. Graphene-based artificial nanopores have attracted considerable attention due to their selective transport of small molecules with confinement down to a subnanometer scale, enabling novel applications in energy storage and conversion, molecular separation, and biomolecular sensing. − A graphene nanopore, as a model ion channel, is a well-defined nanofluidic system with reduced dimensions for exploring ion transport mechanisms, and graphene nanopores can achieve fast ion and water transport featuring the characteristics of low transport resistance and large permeation flux due to their atomic-level thickness. Furthermore, because of its precisely engineerable pore geometry, a graphene nanopore is capable of the highly efficient and selective transport of ions.…”

Enumerating Stable Nanopores in Graphene and Their Geometrical Properties Using the Combinatorics of Hexagonal Lattices

“…9,39,60−62 As mentioned before, Bondaz et al used the concept of PLD as it can capture the protrusions and irregularities of the pore shape. 60 In a similar vein, the properties that we have enlisted can help the screening process of finding suitable pores, albeit in a faster manner. Since PLDs can be seen as a function of the major and minor axes lengths as well as the shape factor, after screening the nanopores using such readily calculated geometric shape properties, the PLDs of the screened pores can be calculated using more expensive methods of optimization and/or image processing.…”

“…Computational screening of nanopores should prove to be a vital tool for theorists in predicting structure−property relationships of nanoporous media for a variety of applications. Recently, Bondaz et al addressed the limitations in screening and understanding the transport characteristics of nanopores (caused by the expensive computational cost imposed by molecular simulations) using rapid screening methods based on pore shape and size, as characterized by the pore limiting diameter (PLD), 60 i.e., the diameter of the largest circle that can fit inside a nanopore. On the other hand, experimentalists may want to examine the atomic structures of nanopores like what they may observe in microscopy studies.…”

“…Before concluding this subsection, we note the advantages of the nanopore searching feature made available here in the context of nanopore design studies using machine learning. ,,− As mentioned before, Bondaz et al. used the concept of PLD as it can capture the protrusions and irregularities of the pore shape .…”

High-Throughput Nanopore Fabrication and Classification Using Xe-Ion Irradiation and Automated Pore-Edge Analysis

“…Instead, semi-analytical estimates of the permeation properties of individual nanopores and entire membranes could prove both reasonably accurate and highly computationally efficient. Although such estimation methods are challenging to implement, individual steps are already being taken toward, for example, rapid screening of nanopores 47 or a detailed analytical formulation of how water molecules behave near nanopores. 48 We believe that further improvements in the on-the-fly conversion of the structural and statistical data into accurate physics-based property estimates should yield software tools that enable a true function-by-design approach to porous 2D membrane fabrication.…”