$re = '/((?=\(\+)\()|[\s+=]|((?<=M)\))/';
$str = 'C5H6 + O = NC4H5 + CO + H
C5H5 + H (+M)= C5H6 (+M)
C5H5 + HO2 = C5H5O(2,4) + OH
';
$subst = "";
$result = preg_replace($re, $subst, $str);
echo "The result of the substitution is ".$result;
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php