The interactions of kerogen with charged mineral entities such as clays in oil shale are important for the development of new processes for extraction of kerogen from oil shales. In this work, the complex 3D structure of Green River Type I kerogen was developed from its seven components or fragments using Siskin's two-dimensional (2D) structure. Sodium (Na)-montmorillonite, one of the minerals identified in the Green River oil shale, was chosen for kerogen and clay mineral interaction study. The seven fragments of the kerogen structure vary in complexity with moities ranging from aliphatic, aromatic and olefinic hydrocarbons to nitrogenous aromatic, aliphatic and ammonical structures. The molecular orientation of each fragment was evaluated using Molecular dynamics (MD) simulations indicating significant non-bonded interactions between clay and kerogen. The simulation results also illustrate the significant non-bonded interactions of Na-montmorillonite clay preferentially with fragments 4, 5, 6, and 7 as compared to fragments 1, 2, and 3. The quantitative values of interactions were compared in the context of the molecular nature and differences between the fragments. These interactions were primarily predominated by van der Waals energy. Also, fragment 7 has the highest interaction with clay. At the same time, when kerogen interacts with clay minerals, there were also strong attractive non-bonded interactions between the kerogen fragments. Fragments 5 and 7 and fragments 6 and 7 have higher interactions between them than other fragments. These interactions were primarily electrostatic in nature. These studies represent a comprehensive analysis of the interactions of the complex 3D structure of kerogen with montmorillonite. The interactions between kerogen and clay mineral and within kerogen fragments provide insight for researchers to develop new methodologies to extract the kerogen economically, efficiently, and environmentally friendly from Green River oil shale. (C) 2017 Elsevier Ltd. All rights reserved.