Unraveling complex molecules

In many research areas of chemistry the studied chemical compounds have unknown structural formulas. Yet molecular simulations are currently used to study their 3D organization. In this paper, the author discusses some of these compounds, which are studied in a wide range of disciplines: Lignin in biochemistry; humic acids, kerogen, and asphaltene in petroleum chemistry; coal in fuel sciences; and amorphous silica gels in materials science. To overcome the problem of determining a structural formula and an initial 3D organization, three approaches can be taken: conventional, deterministic, or stochastic. The authors show that by using a stochastic approach it is possible to generate a sample of 3D molecular models that statistically represents the entire population of all the possible models that can be built from a set of analytical data. He presents a new structure elucidation system called the SIGNATURE (StochastIc GeNerator of chemicAl strucTURE) program, believed to be the first stochastic computer-assisted structural elucidation (CASE) system.