Please help for the moment no way to include chemistry in Mathjax
You need to add the mhchem.js extension to another part of your configuration, namely the TeX part.
Here is a configuration that worked correctly for me (a modification of the 'default' custom configuration on a clean Drupal7/MathJax environment:

MathJax.Hub.Config({
  extensions: ['tex2jax.js'],
  jax: ['input/TeX','output/HTML-CSS'],
  TeX: {
    extensions: ['mhchem.js'],
  },
  tex2jax: {
    inlineMath: [ ['$','$'], ['\\(','\\)'] ],
    processEscapes: true,
    processClass: 'tex2jax',
    ignoreClass: 'html'
  },
  showProcessingMessages: false,
  messageStyle: 'none'
});


My content looked like this:

$2 + 2 = 4$

$\ce{H2O}$


and gave me this as an output:


Hope this helps!