Use r66 of three.js

Code migrated to r66 of three.js. Major change is Face4 is deprecated and you have to use 2 Face3 objects. Also, added the var declarations in the for loops back in. It's a point for debate but in ES5 'strict' mode the code would not work because it requires the variables to be declared before use. Also, the loop vars are scoped to the function they are declared in so should be ok and not conflict with anything else.
I had a look at three.js r67 and r68. r67 renders the molecule but seems to cause issues with the mouse interactions. r68 has changed many of Object3Ds properties to be immutable which seems to cause the molecule not to render and will probably require quite a few code changes.