Or without the  while loop (the file  chem.data holds the data specified in the OP): 
>perl -wMstrict -ne
"print qq{$_\t}, join(qq{\t}, /([A-Z][a-z]?(\d*))(?=.*(\n?))/g);
"
chem.data
CH4N2O
        C
        H4      4
        N2      2
        O
C9H12N2O6
        C9      9
        H12     12
        N2      2
        O6      6
C5H11NO2
        C5      5
        H11     11
        N
        O2      2
C5H4N4O2
        C5      5
        H4      4
        N4      4
        O2      2
C10H11N4O9P
        C10     10
        H11     11
        N4      4
        O9      9
        P
C10H12N4O6
        C10     10
        H12     12
        N4      4
        O6      6
C5H10O5
        C5      5
        H10     10
        O5      5
C5H12O5
        C5      5
        H12     12
        O5      5
C5H10O5
        C5      5
        H10     10
        O5      5
C27H44O
        C27     27
        H44     44
        O
C1694H2993O101
        C1694   1694
        H2993   2993
        O101    101

[download]
Note, however, that this approach:

In reply to Re^2: Recursive capture of a variable number of elements using regexp by AnomalousMonk
in thread Recursive capture of a variable number of elements using regexp by seaver

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.