Need to Write a Code that can find the molecular weight of various compounds

Matthew,

I would try first looking at the Rcdk package. From it sound like what you 
want to do they already have some very efficient code to that. If you don't 
want all of CDK then you could try Rdisop from Bioconductor. The package 
will take a formula and give you it's mass. It won't do a matrix but just 
'sapply' the function.

http://cran.r-project.org/web/packages/rcdk/index.html

http://www.bioconductor.org/packages/2.6/bioc/vignettes/Rdisop/inst/doc/Rdisop.pdf
## code from above link##
 
library(Rdisop)

molecule <- getMolecule("C2H5OH")
getFormula(molecule)

[1] "C2H6O"

getMass(molecule)

[1] 46.04186