Counting Atoms in a Chemical Formula

Ruby is trying to find an easy way to determine the number of atoms in molecular formulas of some chemical structures. For instance, a cell might contain a formula such as C12H10N6F2. In this case the number of atoms is 12 + 10 + 6 + 2 = 30. Ruby has about 300 of these formulas to do and was wondering if there is an Excel formula that can be used to do this.

First, the bad news: There is no easy way to do this.

There; with that out of the way, we can start to look for solutions. The example chemical formula provided by Ruby may lead some to think that counting atoms is a simple process of substituting the alphabetic characters with something else so that just the numeric characters can be evaluated. As an example, here is Ruby's example chemical formula:

C12H10N6F2

If you replace the alphabetic characters with plus signs, you get this:

+12+10+6+2

Looks like a simple formula now, right? This is deceiving, because while it will work in this instance, it may not work at all for Ruby's other chemical formulas. Consider the following chemical formula that many people will be familiar with:

H2O

Doing the same substitution renders this:

+2+

Problem is, there is an implied count of 1 whenever there is a single element—for example, the oxygen element. Thus, H20 is actually 3 atoms.

So now we can come up with a way to simply account for the implied 1, right? Sure; this can be done. It can be done most easily and cleanly with a macro, such as the following user-defined function:

Function CountAtoms(ChemForm As String)
    Dim sNewNum As String
    Dim sTemp As String
    Dim iNewAtoms As Integer
    Dim iTotalAtoms As Integer
    Dim J As Integer

    sNewNum = ""
    iTotalAtoms = 0

    For J = 2 To Len(ChemForm)
        sTemp = Mid(ChemForm, J, 1)
        If sTemp >= "0" And sTemp <= "9" Then
            sNewNum = sNewNum & sTemp
        ElseIf sTemp <= "Z" Then
            iNewAtoms = Val(sNewNum)
            If iNewAtoms = 0 Then iNewAtoms = 1
            iTotalAtoms = iTotalAtoms + iNewAtoms
            sNewNum = ""
        End If
    Next J

    iNewAtoms = Val(sNewNum)
    If iNewAtoms = 0 Then iNewAtoms = 1
    iTotalAtoms = iTotalAtoms + iNewAtoms

    CountAtoms = iTotalAtoms
End Function

In order to use this function in your worksheet, you would simply reference the chemical formula:

=CountAtoms(A1)

If the chemical formula is in cell A1, this function returns the count you desire. It will even work with formulas such as the following:

NaCl
SbF6

Note that these rely on two-character element names, of which there are many. It does require, however, that the second character of a two-character element name not be capitalized.

So, will this approach work with all chemical formulas? Not really; it only works with the simple ones we've covered so far. You see, chemical formulas can get quite complex. Consider the following example:

2H2O

When an initial number appears like this, then the formula is to be multiplied by that value. Thus, instead of the normal 3 atoms in H2O, this formula would have 6 atoms.

It gets worse. Consider the following valid chemical formulas:

Ca3(PO4)2
Al2(SO4)3(H2O)18

Note the parentheses followed by a number. In this nomenclature, the value immediately following the closing parenthesis indicate how many of the molecules within the parentheses are in the larger molecule. Thus, in the second example there are 3 molecules of SO4 and 18 molecules of H2O in the overall molecule. This obviously affects the number of atoms in the entire formula. To compound complexity, parentheses can even be nested:

CH3(C3H4(NH2)2)18CH3

Fun, huh?

This can still be addressed with a more complex macro. Rather than reinvent the wheel here, though, if you are working with complex chemical formulas such as these, you might want to consider using the macros provided at this site:

http://www.vbaexpress.com/kb/getarticle.php?kb_id=670

Note that the macros aren't implemented as user-defined functions. To use them you simply select the cells with the formulas, run the macro, and then the macros modify information in the columns to the right of the selected chemical formulas. Full instructions are included with the code at the above website.

You'll also need to make sure you enable, in the Visual Basic Editor, regular expressions. You do this by choosing Tools | References and then scrolling through the available references to locate the Microsoft VBScript Regular Expressions 5.5 option. Make sure the check box to the left of the reference is selected, then click OK.

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