PageRank as a Collective Variable to Study Complex Chemical Transformations and Their Energy Landscapes

Zhou, Tiecheng; Martinez Baez, Ernesto; Schenter, Gregory K.; Clark, Aurora E.

doi:10.1063/1.5082648

Title: PageRank as a Collective Variable to Study Complex Chemical Transformations and Their Energy Landscapes

Journal Article · Sun Apr 07 00:00:00 EDT 2019 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.5082648· OSTI ID:1525102

Zhou, Tiecheng ^[1]; Martinez Baez, Ernesto ^[1];

^[2]; Clark, Aurora E. ^[1]

WASHINGTON STATE UNIV
BATTELLE (PACIFIC NW LAB)

A reduced set of reaction coordinates are often employed in chemistry to describe the collective change between reactants and products within the context of rare event theories and in the exploration of energy landscapes. While incredibly powerful, use of these collective variables becomes increasingly challenging as the systems under study become more complex. Recent advancement of new descriptions of collective molecular coordinates have included PageRank (PR) analysis of the network of interactions about molecules and atoms within a system. Herein, PR is developed as a continuous variable that not only captures chemical transformations but can also be employed as a collective variable for a process that could span a highly dimensional energy surface. The derivatives of PR with respect to atomic coordinates are presented, and subsequently combined with forces during a chemical transformation within biased molecular dynamics sampling simulations to create the potential of mean force (PMF). This technique is demonstrated for two reactions: 1) the transformation of tetrahedral [Al(OH)4]-(aq) to octahedral [Al(OH)4(H2O)2]-(aq), and 2) the formation of contact ion pairs (CIPs) and solvent separated ion pairs (SSIPs) of Na+ and OH- in bulk water. Comparison of the behavior of the PR collective variable in both examples reveals that the ability of the PR to resolve local versus extended configurational attributes is tuned by the size of the network employed. This is a unique feature of PageRank that enables control over the resolution of the PMF that is produced.

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Research Organization:: Energy Frontier Research Centers (EFRC) (United States). Interfacial Dynamics in Radioactive Environments and Materials (IDREAM); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1525102

Report Number(s):: PNNL-SA-132298

Journal Information:: Journal of Chemical Physics, Vol. 150, Issue 13

Country of Publication:: United States

Language:: English

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