Googling Helps Map H-Bonding Networks

Computational chemists have developed a data-mining tool that takes advantage of Google’s PageRank numerical weighting algorithm to analyze the organizational structure and dynamics of simulated hydrogen-bonded solutions (J. Comput. Chem., DOI: 10.1002/jcc.22917). Google and other search engines use PageRank to determine how relevant a website hit is to a search and to prioritize the results. Aurora E. Clark of Washington State University, along with Barbara Logan Mooney and L. René Corrales of the University of Arizona used R, a statistical computing programming language, to create software scripts they call moleculaRnetworks to analyze the solvation spheres of water molecules around a solute. The scripts use PageRank to track dynamical changes in the hydrogen-bonding network and identify geometric shapes adopted by the solvent around a solute. The study, which appears to be the first time PageRank has been applied to chemical problems, “has turned out to be a nice way to fold modern Internet informatics into the field of computational chemistry,” Clark says. She believes the program could be used in simulations of other time-dependent phenomena, including nucleation and self-assembly.