Location: Spark 227

Streaming link: https://zoom.us/j/999902371

Advances in Graph Theory Methods to Understand Chemical Behavior

Presented by: Dr. Aurora Clark, Department of Chemistry, Washington State University

Abstract

Graph theoretical approaches for characterizing the structure and dynamics of condensed phase systems have rapidly expanded in the last five years.¹ Such methods utilize network analysis algorithms to study the behavior of covalent or intermolecular interactions and can include a large array of algorithms including Google’s PageRank,² and the Dijkstra algorithm that underpins nearly all routing software.³ Applications of these methods have helped reveal new correlating relationships in many complex systems, including concentrated electrolytes,^4-5 liquid:liquid phase boundaries,^5-6 and in solvent confinement.^7-8 More recent advances leverage the topological patterns of these chemical networks as new collective variables for potential of mean force simulations – increasing the tools available to study highly dimensional energy surfaces and reaction mechanisms.⁹

References

• Clark, A. E. Intermolecular Network Theory: A General Approach for Understanding the Structural and Dynamic Properties of Liquids and Solutions. In Annual Reports in Computational Chemistry; Dixon, D. A., Ed.; 2015; pp 313–359
• Hudelson, M.; Mooney, B. L.; Clark, A. E. Determining Polyhedral Arrangements of Atoms Using PageRank, Journal of Mathematical Chemistry 2012, 50, 2342.
• Ozkanlar, A.; Clark, A. E. ChemNetworks: A Complex Network Analysis Tool for Chemical Systems, Journal of Computational Chemistry, 2014, 35, 495-505.
• Kelley, M.; Donley, A.; Clark, S.; Clark, A. E. Structure and Dynamics of NaCl Ion Pairing in Solutions of Water and Methanol Journal of Physical Chemistry B 2015, 119, 15652-15661.
• Ghadar, Y.; Christiansen, S. L.; Clark, A. E. Influence of Aqueous Ionic Strength Upon Liquid:Liquid Interfacial Structure and Dynamics, Fluid Phase Equilibria, 2016, 407, 126-134.
• Ghadar, Y.; Parmar, P.; Samuels, A.; Clark, A. E. Solutes at the Liquid:Liquid Phase Boundary – Solubility and Solvent Conformational Response Alter Interfacial Microsolvation Reactions, Journal of Chemical Physics, 2015, 142 , 104707
• Wang, C.; Bai, P.; Siepmann, I.; Clark, A. E. Deconstructing hydrogen bond networks of solvents confined in nanoporous materials: Implications for alcohol-water separation Journal of Physical Chemistry C 2014, 118, 19723-19832.
• Zhou, T.; McCue, A.; Ghadar, Y.; Bako, I.; Clark, A. E. On the Behavior of Capillary Wave Fronts and Their Role in Defining Interfacial Regions of Water, Journal of Physical Chemistry B, 2017, DOI:1021/acs.jpcb.7b07406
• Zhou, T.; Martinez-Baez, E.; Schenter, G.; Clark, A. E. PageRank as a collective variable to study complex chemical transformations, Journal of Chemical Physics, 2018,