Sampling molecules
While finding all the chemical structures that match a given set of
physico-chemical analytical data seems to be an intractable computational
problem, it is possible to use stochastic techniques to generate a sample
of three-dimensional molecular models that is statistically representative
of the entire population of potential models.
Performing a structure elucidation using a stochastic approach is similar
to studying the conformational space of a molecule using stochastic methods
such as Monte Carlo or Genetic Algorithm methods. However, in the
case of structure elucidation the search space is no longer composed of
the ensemble of all possible conformations, but is composed of the finite
number of possible structural isomers that can be constructed from a set
of analytical data.
We have demonstrated that by using a stochastic approach, it is possible
to generate a sample of three-dimensional molecular models that statistically
represents the entire population of all the possible models that can be
built from a set of analytical data.
We have also designed a stochastic algorithm based on the simulated
annealing method that searches chemical structures with desired properties.
Theoretically, the algorithm was shown to be efficient (i.e., polynomial-time).
Practically, the algorithm performs remarkably well even in very large
search space sizes (up to 1032).
The above sampling techniques are being applied to investigate molecular
structures studied in polymer science, biochemistry, geochemistry, fuel,
petroleum, and materials sciences. The proposed stochastic techniques
appear to be essential tools for anyone who wants to use molecular modeling
techniques for structurally unresolved molecular compounds.
Papers
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Faulon. J. L.. Stochastic Generator of Chemical Structure.
2. Using Simulated Annealing To Search the Space of Constitutional Isomers.
J. Chem. Inf. Comput. Sci. 1996, 36, 731-740.
Abstract (.html). Full paper (.ps.gz).
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Faulon, J. L. Unraveling complex molecules. CHEMTECH
1995, 25, 16-23.
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Faulon. J. L.. Stochastic Generator of Chemical Structure.
1. Application to the Structure Elucidation of Large Molecules. J.
Chem. Inf. Comput. Sci. 1994, 34, 1204-1218.
Abstract (.html). Full paper (.ps.gz).
Papers (applications)
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Kowaleski I., Vandenbroucke M., Faulon J. L., Taylor J., Behar F., Huc
A. (1996). Asphaltene Molecular Modeling of Boscan Crude Oil, Revue de
l'I.F.P 51, 161-170.
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Kowaleski I., Vandenbroucke M., Taylor J., Faulon J. L., Huc A. (1996).
Preliminary Results on Molecular Modeling of Asphaltene using Structure
Elucidation Programs in Conjonction with Molecular Simulation Programs,
Energy&Fuel 10, 97-107.
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Boduszynski, M. M., Faulon J. L. (1996) Molecular Structure Elucidation
of Cycloalkyl-coronenes found in Hydrocracked Oils, Proceedings of the
Dhahran 1996 Lab. R&D Center Technical Exchange Meeting.
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Boduszynski, M. M., Rechsteiner, C. E., Grudoski D. A., Iwamoto J. D.,
Faulon J. L. (1996) The Effect of Molecular Structure on Molecular Weight
- Boiling Point Relationship for Petroleum Fractions, Proceedings of the
Dhahran 1996 Lab. R&D Center Technical Exchange Meeting.
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Pohl P. I., Faulon J. L., Carlson G. A., Smith D. M. (1996). A Computer
Study of the Pore Structure of Imogolite, Lamgmuir, 18, 4463-4468
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Faulon J. L., Loy D. A., Carlson G. A., and Shea K. J. (1995). Computer-aided
Structure Elucidation for Arylsilsesquioxane Gels, Computational Materials
Science 3, 334-346.
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Pohl P. I., Faulon J. L., Smith D. M. (1995). Molecular Dynamics Computer
Simulations of Silica Aerogels, J. Non Cryst. Solids 186, 349-355.
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Faulon J. L., Carlson, G.A., and Hatcher P. G. (1994). A Three-Dimensional
Model for Lignocellulose from Gymnospermous Wood, Org. Geochem. 211, 1169-1179.
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Faulon, J.L., and Hatcher, P. G. (1994). Is There Any Order in the Structure
of Lignin ?, Energy & Fuels 8, 402-407.
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Faulon J. L. , Mathews J. P., Carlson G. A., and Hatcher P. G. (1994).
Correlation Between Microporosity and Fractal Dimension of Bituminous Coal
Based on Computer-Generated Models, Energy & Fuels 8, 408-414.
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Faulon J. L. , Carlson G. A., and Hatcher P. G. (1993). Statistical Model
for Bituminous Coal: A Three-Dimensional Evaluation of Structural and Physical
Properties Based on Computer-Generated Structures, Energy & Fuels 7,
1062-1072.
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Faulon J. L., Hatcher P. G. , Carlson, G.A., and Wenzel K. A.(1993). A
computer-aided Molecular Model for High Volatile Bituminous Coal, Fuel
Processing Technology 34, 277-293.
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Hatcher, P. G., Faulon J. L., Clifford D. A., Mathews J. P. (1993) A Three-dimensional
Structural Model for Humic Acids from Oxidized Soil. Proccedings of the
6th IHSS Int. Meeting, Elsevier, Amsterdam, 436-446.
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Faulon J.L., Vandenbroucke M., Drappier J.M., Behar F., and Romero M. (1990).
3D Chemical Model for Geological Macromolecules, Org. Geochem. 16, 981-993.
Page maintained by Jean-Loup
M. Faulon , last updated 10/14/97