There seem to be several packages out there dealing biological and chemical data and also KNIME has a strong footing in that community.
There is this R package you might be able to use from KNIME.
http://www.bioconductor.org/packages/release/bioc/vignettes/ChemmineR/inst/doc/ChemmineR.html
Maybe if you provide us with sample data and an idea what result you would want someone might be able to help.