Worm's Eye View: Molecular Worm Algorithm Navigates Inside Chemical Labyrinth

With the passage of a molecule through the labyrinth of a chemical system being so critical to catalysis and other important chemical processes, computer simulations are frequently used to model potential molecule/labyrinth interactions. In the past, such simulations have been expensive and time-consuming to carry out, but now researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) have developed a new algorithm that should make future simulations easier and faster to compute, and yield much more accurate results.

"Currently the major limiting factor in running molecular simulations for a large number of structures before they can be screened for useful materials is the need to visually analyze the structures to set up successful simulations," says Maciej Haranczyk, a computational chemist and a 2008 Glenn T. Seaborg Fellow in Berkeley Lab's Computational Research Division. "With our approach, such structural analysis can be done automatically, which speeds up the whole process of material screening."

Haranczyk is co-author of a paper that appears in the Proceedings of the National Academy of Sciences entitled: "Navigating molecular worms inside chemical labyrinths." The other author of this paper is James Sethian, who heads the Mathematics Group of Berkeley Lab's Computational Research Division, and is also a professor in the Mathematics Department of the University of California, Berkeley

A key to the success of this new algorithm was its departure from the traditional treatment of molecules as hard spheres with fixed radii. Instead, Haranczyk and Sethian constructed "molecular worms" from blocks connected by flexible links. These molecular worms provide a more realistic depiction of a molecule's geometry, thereby providing a more accurate picture of how that molecule will navigate through a given chemical labyrinth, as Sethian explains.

"In practice, most molecules of interest, even the simplest solvents or gases, rarely have a spherical shape, and treating molecules as such may lead to errors," he says. "Our molecular worms are able to change shape during the traversing of a chemical labyrinth, which allows them to reach areas not accessible to either a single large spherical probe or a rigid real-shape probe. This significantly extends the range of probes and structures that can be efficiently examined."

As a molecule navigates through a chemical system, its access to a particular site or place within that system determines the extent to which catalysis and other chemical reactions may occur. Many of these critical sites are either buried in clefts, pockets or hidden cavities, or else represent channel systems. The accessible volume of a chemical system – the free volume available to a penetrating molecule – is also critical to the system's physical properties, including diffusion, viscosity and electrical conductivity. Predicting whether a molecule will be able to traverse through a given chemical labyrinth is the first question that a simulation must answer, followed by identifying the shortest transverse route, finding the largest probe that can transverse though the system, and calculating accessible volume.

A key to the success of this new algorithm was its departure from the traditional treatment of molecules as hard spheres with fixed radii. Instead, Haranczyk and Sethian constructed "molecular worms" from blocks connected by flexible links. These molecular worms provide a more realistic depiction of a molecule's geometry, thereby providing a more accurate picture of how that molecule will navigate through a given chemical labyrinth, as Sethian explains.

"In practice, most molecules of interest, even the simplest solvents or gases, rarely have a spherical shape, and treating molecules as such may lead to errors," he says. "Our molecular worms are able to change shape during the traversing of a chemical labyrinth, which allows them to reach areas not accessible to either a single large spherical probe or a rigid real-shape probe. This significantly extends the range of probes and structures that can be efficiently examined."

As a molecule navigates through a chemical system, its access to a particular site or place within that system determines the extent to which catalysis and other chemical reactions may occur. Many of these critical sites are either buried in clefts, pockets or hidden cavities, or else represent channel systems. The accessible volume of a chemical system – the free volume available to a penetrating molecule – is also critical to the system's physical properties, including diffusion, viscosity and electrical conductivity. Predicting whether a molecule will be able to traverse through a given chemical labyrinth is the first question that a simulation must answer, followed by identifying the shortest transverse route, finding the largest probe that can transverse though the system, and calculating accessible volume.

SOURCE: Berkeley National Laboratory