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I tried to look around for an answer to this problem but don't know how to ask the proper question in a search engine. I've been working on a song and realized recently that while I had been working on the song in the key of Em (E, F#, G, A, B, C, D) I had accidentally placed D# notes in several of my melodies. The confusing part is it sounds fine and I didn't even notice until I looked closer. What's more, if I change them to D it sounds off key and if I change them to E it just sounds wrong for what the melody is supposed to be doing. I don't have much music theory knowledge but this confused what I thought I knew. Am I misunderstanding something here? Any help and clarification would be appreciated.

Your confusion is understandable because you have the choice of using one, or a combination, of three minor scales: the natural minor, the harmonic minor or the melodic minor. In using a D# you have strayed from the natural minor scale to the melodic minor scale, and this scale has worked for you.

The natural minor scale flattens the 3rd, 6th and 7th degrees of the parallel major scale. The harmonic minor scale flattens the 3rd and 6th. The melodic minor (ascending) only flattens the 3rd, but when descending it is identical to the natural minor, flattening the 3rd, 6th and 7th. The jazz melodic minor just flattens the 3rd, ascending and descending.

These scales are all legitimate minor scales (there are others too). At present you seem to prefer that semitone sound between D# and E, and that's fine.

D# makes a nice lower neighbor to E. Likewise, in E-minor, the dominant (B) often has its third raised at cadence points. Minor keys (at least in classical theory) have two mutable notes; scale steps 6 and 7 may be raised to make voice leading smoother or just because it sounds good.

You'll most likely find that the chord used where D♯ fits better is B major, or B7. That has the D♯ in it. The D ♮ will fit in other places, notably when going from an Em chord to an Am. It's the reason centuries ago that the natural minor scale morphed into the harmonic minor, with a raised leading note ( here, the D♯), and later, because there was then a great big jump of a tone ane a half created, the 6th note of that natural minor got sharpened too, to remove a big jump.

All the minor scales have the same first five notes, but the melodic minor (classical) has the same 6 and 7 as the parallel major scale.