You have done well to notice the link between nature and the evil inherent in the play. This is a key theme of this excellent tragedy as it is in Julius Caesar. Clearly, the most notable incident of nature itself matching the tone of the play comes at the very beginning, with the thunderstorm in which we are introduced to the witches. Note how this sets the tone for the rest of the play: we are plunged immediately into a world of darkness, of primeval power and strength as reflected by the lightning and thunder.
However, for a far more interesting example of what you are talking about, I would want to talk about the beginning of Act I scene 6, when Duncan, much like a lamb to the slaughter, approaches Macbeth's castle. Note what he says about it as he comments, rather naively, on its beauty:
This castle hath a pleasant seat; the air
Nimbly and sweetly recommends itself
Unto our gentle senses.
Note the dramatic irony of the passage: we have just seen the Macbeths plotting to kill Duncan, and yet to him, this castle seems to be a place of rest and peace. Now, it is important to remember that the theme of appearance vs. reality is incredibly important in this play. In the previous scene, we have just scene Lady Macbeth counsel her husband to "look like th'innocent flower, / But be the serpent under't." Characters who appear to be good on the surface are actually evil beneath, and this is an excellent example of where nature itself conspires with Macbeth and his wife to deceive the King and lead him in to his doom.