3-D structure of a local minimum of the Siskin model of oil shale kerogen using the RHF/STO-3G method

Kerogen is a mixture of organic chemical compounds that make up a portion of the organic matter in sedimentary rocks. It is insoluble in normal organic solvents because of the huge molecular weight (upwards several thousand Daltons). When heated in the Earth's crust, (oil window ca. 6 ∞-120∞C; gas window ca.120∞-150∞C) some types of kerogen release hydrocarbons in the form of crude oil or natural gas, collectively known as fossil fuels. Kerogens can also be found in rocks such as shale, as oil shale deposits. The objective of this study is to determine the theoretical 3-D structure of kerogen and its interaction with the inorganic matter of the rock for the purpose of identifying suitable means of isolating kerogen from oil shales. The RHF/STO-3G calculation of this model (1702 atoms) involves 4458 basis functions and ran on 32 quad-core nodes with 8 Gbytes of memory per node. Each optimization step takes about 5 hours to finish. Multiple initial 3-D structures are obtained using the Simulated Annealing procedures followed by ab initio optimization to identify suitable structures. This annealing/optimization process is repeated until a plausible set of the lowest energy structures is gathered. In this image,carbons are colored cyan, oxygens are colored red, nitrogens are colored blue, sulfurs are colored yellow, and hydrogens are colored gray. The tubes represent the molecule's backbone and the spheres represent the atoms. The image is prepared using VMD.