Navigating molecular worms inside chemical labyrinths

Abstract

Predicting whether a molecule can traverse chemical labyrinths of channels, tunnels, and buried cavities usually requires performing computationally intensive molecular dynamics simulations. Often one wants to screen molecules to identify ones that can pass through a given chemical labyrinth or screen chemical labyrinths to identify those that allow a given molecule to pass. Because it is impractical to test each molecule/labyrinth pair using computationally expensive methods, faster, approximate methods are used to prune possibilities, ''triaging'' the ability of a proposed molecule to pass through the given chemical labyrinth. Most pruning methods estimate chemical accessibility solely on geometry, treating atoms or groups of atoms as hard spheres with appropriate radii. Here, we explore geometric configurations for a moving ''molecular worm,'' which replaces spherical probes and is assembled from solid blocks connected by flexible links. The key is to extend the fast marching method, which is an ordered upwind one-pass Dijkstra-like method to compute optimal paths by efficiently solving an associated Eikonal equation for the cost function. First, we build a suitable cost function associated with each possible configuration, and second, we construct an algorithm that works in ensuing high-dimensional configuration space: at least seven dimensions are required to account for translational, rotational, and internal degrees of freedom. We demonstrate the algorithm to study shortest paths, compute accessible volume, and derive information on topology of the accessible part of a chemical labyrinth. As a model example, we consider an alkane molecule in a porous material, which is relevant to designing catalysts for oil processing.fast marching methods ͉ robotic navigation ͉ accessible volume

Chemical Hieroglyphs: Abstract Depiction of Complex Void Space Topology of Nanoporous Materials

“…One has to consider these shortcomings when analyzing a T-ring before drawing any conclusions. At this moment, it is worth mentioning that we have recently proposed an advanced approach, 30 in which a spherical probe is replaced with one resembling the shape and flexibility of a "real" molecule, a complex object built from solid blocks connected by flexible links. Such advanced probes are able to change shape during the traversal of a porous material, reaching areas not accessible to either a single large spherical probe or rigid molecular-shaped probes.…”

Accelerating analysis of void space in porous materials on multicore and GPU platforms

“…Automatic detection of internal cavities has been explored in the context of zeolites [20] -using 'largest void cylinders' and spherical 'cages' -and proteins [21], and the more general question of finding possible pathways through chemical systems has been addressed in both proteins [22] and materials [23][24][25][26] . All of the aforementioned references, with the exception of [17], attempt to study paths of a spherical probe representing the molecule inside a convex hull constructed from atoms of a protein or materials framework.…”

“…In our approach, we used a partial differential equations (PDE)-based front propagation technique to segment out channels and inaccessible pockets of a periodic unit cell of a material. Unlike other approaches that approximate guest molecules with a spherical probe, the general framework of our approach [17] allows guest molecules to have more complex and flexible shapes.…”

“…The new 4 capabilities offered by our approach [16,17] come at the price of increased computational cost associated with the discretization and analysis of the configuration space of a guest molecule inside the material.…”

High-Throughput Characterization of Porous Materials Using Graphics Processing Units

“…Accordingly, we have recently developed algorithms for the automatic segmentation of void space (into accessible and inaccessible regions) and the exclusion of pockets. 37 The original algorithms 37 relied on partial differential equation (PDE)-based front propagation techniques, by which the grid representing the guest-accessible positions (or, in the case of complex nonspherical probes, guest accessible orientations at each position 38 ) can be segmented. There are numerous advantages to a PDE-based segmentation algorithm, including the approximation of paths of least resistance between certain positions within the structure, which can give insights regarding diffusion.…”