Chemical scheme calculator
A couple of format rules like:


Is a good practice declare first and then use it. Is not a big deal, but is a good practice.
Try to use, Pascal Case for constructors, and camelCase for methods.
You can replace some repeated function with inheritance javascript


Also, try to don´t abuse of the this. In javascript is a little tricky and can be changed depending of the context.
For default values use 

var something = original Value || default Value;


also, last thing most important for your calculator, take a look to the javascript floating points troubles maybe you can get wrong results.