3D Model Structures of Oil Shale Kerogen and Sand Tar Asphaltenes
Ian S.O. Pimienta1, Anita M. Orendt1, Ronald J. Pugmire2, and Julio C. Facelli1,3
1Center for High Performance Computing and 2Departments of Chemistry and of Chemical and Fuels Engineering and 3Biomedical Informatics, University of Utah, Salt Lake City, Utah 84112
Introduction
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 large molecular
weight (upwards of several thousand Daltons). When
heated in the Earth’s crust (oil window ca. 60 ° - 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.
Asphaltenes are molecular substances found in
crude oil. They are one of the major components in
heavy oils, tar sands, and biodegraded oils (15%)
which are expected to feature prominently in the
world’s energy mix in the decades to come.
The objective of this study is to develop 3D
structures of kerogens and asphaltenes that can be
used to model their interaction with the inorganic
matter of the rock for the purpose of identifying novel
means of extracting them with a smaller carbon
footprint.
Results
3D globular local structures of kerogen were
obtained due to folding of the long aliphatic
chains in the Siskin model.
From a molecular standpoint, separation of the
seven distinct molecular units in the Siskin
model could be difficult due to lack of
accessibility of the smaller fragments from the
surface.
The flexible bridge between aliphatic and
aromatic groups in asphaltene molecules gives
rise to several conformational structures.
The figure consists of 12 kerogen units (20402 atoms). The atom colors are as follows: C - teal,
O - red, N - blue, S - yellow, H - gray. The tubes represent the molecule’s backbone and the
spheres represent the atoms.
using the molecular mechanics packages in
HyperChem (MM+ force field) and the RHF/STO3G level of theory in GAMESS.
stacking in asphaltene units is the preferred
orientation due to strong - interactions.
Molecular dynamics simulations are presently
underway to determine how many asphaltene
units per stack are present.
Computational Details
All structure minimizations were performed
Initial calculations suggest that parallel
Evaluation of 3D molecular models will be based
Campana
Mid-Continent U.S.
San Joaquin Valley
on ability to use model to reproduce
experimental data on actual kerogen and
asphaltene samples.
The simulated annealing procedure was
employed to generate several monomer
conformations.
Models consisting of up to 12 kerogen units
were generated.
Acknowledgements: An allocation of computer time from the Center for
Loydminster W.
Maya
Heavy Canadian
Several different 3D asphaltene models were
created based on available literature 2D models
of asphaltenes from different sources.
The 3D images were generated using VMD.
Parallel Stack
Anti-parallel Stack
Inverted Stack
The atom colors are as follows: C - gray, O - red, N - blue, S - yellow, H - white. The tubes represent the
molecule’s backbone and the spheres represent the atoms.
High Performance Computing at the University of Utah is acknowledged. This
work is supported by a grant from the U.S. Department of Energy, National
Energy Technology Laboratory. DE-FE0001243